Clone LD20239 Report

Search the DGRC for LD20239

Clone and Library Details

Library:LD
Tissue Source:Drosophila melanogaster embryo
Created by:Ling Hong
Date Registered:1997-12-04
Comments:Constructed using Stratagene ZAP-cDNA Synthesis kit. Oligo dT-primed and directionally cloned at EcoRI and XhoI in BlueScript SK(+/-)
Original Plate Number:202
Well:39
Vector:pBS SK-
Associated Gene/TranscriptRcd6-RA
Protein status:LD20239.pep: gold
Preliminary Size:2563
Sequenced Size:2559

Associated Genes

Associations are from manual ordering of a clone or by a periodic analysis.
Gene Date Evidence
CG11175 2001-01-01 Release 2 assignment
CG11175 2001-10-10 Blastp of sequenced clone
CG11175 2003-01-01 Sim4 clustering to Release 3
CG11175 2008-04-29 Release 5.5 accounting
CG11175 2008-08-15 Release 5.9 accounting
CG11175 2008-12-18 5.12 accounting

Clone Sequence Records

LD20239.complete Sequence

2559 bp (2559 high quality bases) assembled on 2001-10-10

GenBank Submission: AY061284

> LD20239.complete
AGTGGTCGCAGAGTCGTTCGGCGAACCAAGTTCGTTTCCTCAGTCTTTCG
AATTTCACTTTTAACCGTTTGCAAGCGCGCCAAGTTGAAGCGTACGCGTA
CCGTTAGCGCGGCACGTTACGAACACCAACCTAGCATGACACCGCTCAAT
TGGGCCGCTACTTAACGCTTTCATTCAACCCAGAAGAGGTCTGGACTCGA
AACCCATTCGAACATAAACCAAGAACTAGAACACATCGCATCGCATCGTA
TCGCATCGCACCACTGGCCTCCTCCTTTGAAAAAGGGGAACCAAGGCCAC
CCTCCCGCTAGCCAGCATAATTTCTCTTGAAAAACCGCATTCACACATTT
GCTTCACACCACAACCGCAACAACCGAATAACACGAATAATGAATTATCA
GAAGGCCAGTGAAAAGCAGTCGTCGTCCTCATTGAAGAAGCGGCCGCCGG
GCAACGGCAATAGCATACAAAACTTTTGGAACGATCGCATTATGGAGCGC
TTCATAAAGGCGAATCTATTCATTATCTGCTGCGTGGTGGCGGTTCTATT
GCTGATCGTCTATCTGGGTGCCTTCTCGTGTGAGGTCTCGTGGATACTGG
AGGCCCACGGCGAGCTGCCCTTCGCCGCCTACACGCTCTGCTCGCTCTAC
TTTGTCATGTTCGTGGCCACCACGATCCTTATCCACGGCCTGGTCAGCGG
ACTCTGCTGGCCGTTGTTCGCCTGGTCGGGCATCATCGGTCTCCTCTCAA
TTCCAGAGCTGGTCTTTGTCATGATCATGACCACACAGCACTGGGGTCTG
CAATCTGTGCATGGATTAACGGAGCTCACCTCCTACCTGATTCGCCTCAT
CATCAACTGCTTCGCGCTGATCTGTGTGATTCCCACGGGCATCAGGTGGC
GACGGGAGACTCAGGTGTTGAGTCAGCTGCAAGGATTGGCCACCAGACTT
TCCCTGCAGACTCCAGCGCCCAGTGTGCCCATTACAAAGGCAGATTCCCG
GCGATCCAGCCAGCGGCTAAGTGGATTCGAGAATGCCGGCTACCAGCTGT
GCGATGAAACAGCTTCCAAGTTGCCACTAGGGCCAGGAATGGGACTGGGC
ATGAACAACCAGTGTGGAGGCAGTCAAGCATTTGGCTCGCAGAACGAATT
CAACGCCAGCATGTTTGCACCCGCATTGGCACAGCAGTTCAACAATGCCA
CGTTGATGCAGCGCGGCGGAACAGGCGGAGCAGGTGGTGGTCATCGCGCC
CAGTCGCTGATGGATCTGCGCTGCACTCTGCCCGGCATGTACAATCCACG
ACATGTGCTCGATACGGAGGATAAAAACGCCAAGTACTTCAACATCACCA
TCGACGATTTGAAGAACAATCTCCACGACTCGCACCGACCATCGCCGCCT
TCGCTGATCGGTTCCACCAGCAACGATCCCATCTACTGCTCCATTGAGCC
CAAGCAGTTGACACCGCCACCGGCACAGCAGAGGAGCCACCATCGTCCAC
GCGGCACACACAAGCAGCCACCACCGGGTAAACTGTCCCGGAATTGCGTA
TCCCTGGAGAACCTTGACGGGATCAGCAAGGTGCAGAATGATCTGACCGC
CTACGGGAACAATCTACTCCAGAACTACACGCAGCAGCAGCAGTATTACC
TGGCCATGCTGCTTCACCAGCAGCAGCAGCAACAGCTGCACCACCAGCAG
GCTGGCGGCATTTACCGCAGGCCATCCAATTGCAGCTCCACTGGCGGATT
CGCCGGCACCGTGCTGGCCCAGCCGATGCAGCGACGCGGCTCCACGCACA
GCCAGCAGATGCAGTATTACGGGGGCTTTGGCTATGCCAACTACACCAAT
CCGTACATCACGGCCAACAGCAAGTTGTCGCTGGGCAACGAGTCCGACGA
TTACCGGAAGTACCGCGATGTGGCTCTTTGAGTCCGTTTTTTTGGTTCTG
GAAACCGGATCCCAATCGATCATCAGTCAGCGTTTAGGTTAAGCTCACTA
GTTGTAGGATATGCTCGATCTAGAATGAGATTCCTCGGAATAACGACCAA
AGAGCCACAAACTAACTCAGTTTCAGTTCGTAGACTAACGTTACACTGCG
AGAATCGTATAGCGCGTTTATGCGCCAGTCAATTTGTAGCTTAAATGGGT
CTGCATTCAGTTTTATTTGCTTTACTGAATAACACGACCTATTTGCAAAT
AAAAGTGTACTAAATATGAGACTCCATGGGGATATAATTTTATATGCAAA
TAAAAGTAATCGTAATAGTAAATATCACGAAATATCAGACGTACTCAAAA
ATATAAATAGATATTTCTAAAACAAACAAATATCAAAAAGCATACCCCCC
CAATAAGAGAGGCACTGTATGAAAATTGCCCAAGTCTAGTTCTAAGAATC
GAACACAAATGAACATTGACATTCATTGTTTATTATAGTTAATAGGAATA
CGAATAACAATACTCTGATCGACAGTCTAACCATCCACAGATCAAAAAGT
GTACATACTTGTAATAAAAGGCGTAACTGTTTTCTCACTTGAAAAAAAAA
AAAAAAAAA

LD20239.complete Blast Records

Blast to MB8.fasta performed 2010-07-15 20:58:26
Subject Length Description Subject Range Query Range Score Percent Strand
Rcd6-RA 2631 Rcd6-RA 91..2631 1..2541 12705 100 Plus
Rcd6-RB 3168 Rcd6-RB 751..3168 124..2541 12090 100 Plus
CG16742.a 4644 CG16742.a 4512..4644 2544..2412 665 100 Minus
Rcd6-RB 3168 Rcd6-RB 67..189 1..123 615 100 Plus
Blast to d_melanogaster_OreR.fa performed 2019-03-16 03:58:36
Subject Length Description Subject Range Query Range Score Percent Strand
chr2R 21145070 chr2R 16514890..16516638 2541..794 8380 98.7 Minus
chr2R 21145070 chr2R 16517403..16517833 554..124 2125 99.5 Minus
chr2R 21145070 chr2R 16516744..16516985 795..554 1195 99.6 Minus
chr2R 21145070 chr2R 16520064..16520186 123..1 615 100 Minus
Blast to dmel-all-all_noncoding-r5.12.fasta performed on 2010-04-22 19:07:32 has no hits.
Blast to na_all.dmel.RELEASE6 performed 2019-03-16 03:58:31
Subject Length Description Subject Range Query Range Score Percent Strand
2R 25286936 2R 20628183..20629933 2544..794 8755 100 Minus
2R 25286936 2R 20630684..20631114 554..124 2155 100 Minus
2R 25286936 2R 20630025..20630266 795..554 1210 100 Minus
2R 25286936 2R 20633351..20633473 123..1 615 100 Minus
Blast to na_arms.dmel.RELEASE6 performed 2011-12-12 22:17:20
Subject Length Description Subject Range Query Range Score Percent Strand
2R 25260384 2R 20629382..20631132 2544..794 8755 100 Minus
2R 25260384 2R 20631883..20632313 554..124 2155 100 Minus
2R 25260384 2R 20631224..20631465 795..554 1210 100 Minus
2R 25260384 2R 20634550..20634672 123..1 615 100 Minus
Blast to na_te.dros performed 2019-03-16 03:58:34
Subject Length Description Subject Range Query Range Score Percent Strand
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6792..6918 1612..1740 189 63.8 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6750..6825 1623..1699 175 71.4 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6715..6805 1611..1700 172 69.6 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2317..2417 1596..1700 163 65.7 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 1493..1587 1605..1698 157 65.6 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6845..6913 1632..1700 156 69.6 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6724..6838 1583..1700 149 63 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6717..6858 1549..1699 147 61.2 Plus
roo 9092 roo DM_ROO 9092bp 1077..1163 1612..1698 147 63.2 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2559..2662 1594..1699 146 64.8 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2308..2384 1623..1700 144 66.7 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2440..2531 1612..1700 137 64.1 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6720..6784 1636..1700 136 67.7 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2724..2957 1636..1873 134 55.4 Plus
gypsy11 4428 gypsy11 GYPSY11 4428bp 855..1015 1543..1705 134 57.8 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2310..2392 1659..1740 133 68.6 Plus
roo 9092 roo DM_ROO 9092bp 1082..1144 1632..1700 133 71 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2345..2476 1567..1699 130 58.2 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 6722..6923 1659..1871 130 56.5 Plus
Dvir\TART 8500 Dvir\TART TARTVIR 8500bp 2778..2871 1601..1698 127 65.7 Plus
roo 9092 roo DM_ROO 9092bp 1085..1120 1665..1700 126 83.3 Plus
Dvir\Het-A 6610 Dvir\Het-A HETAVIR 6610bp 3210..3334 1584..1710 124 59.4 Plus
TART-B 10654 TART-B DM14101 10654bp Derived from U14101 (g603662) (Rel. 42, Last updated, Version 1). 67..228 1572..1736 116 60.1 Plus
TART-B 10654 TART-B DM14101 10654bp Derived from U14101 (g603662) (Rel. 42, Last updated, Version 1). 9097..9258 1572..1736 116 60.1 Plus

LD20239.complete Sim4 Records

Sim4 to d_melanogaster_OreR.fa performed 2019-03-16 03:59:29 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
chr2R 16514890..16515731 1701..2541 99 == Minus
chr2R 16515802..16516637 795..1630 98 <- Minus
chr2R 16516745..16516984 555..794 99 <- Minus
chr2R 16517403..16517833 124..554 93 <- Minus
chr2R 16520064..16520186 1..123 100   Minus
Sim4 to dmel-all-CDS-r5.12.fasta performed 2008-12-08 18:54:35 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
CG11175-RA 1..1542 390..1931 100   Plus
Sim4 to dmel-all-CDS-r5.32.fasta performed 2011-03-16 20:57:32 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
Rcd6-RB 1..1542 390..1931 100   Plus
Sim4 to dmel-all-CDS-r5.52.fasta performed 2013-08-04 07:10:30 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
Rcd6-RA 1..1542 390..1931 100   Plus
Sim4 to dmel-all-CDS-r5.9.fasta performed 2008-07-21 21:40:30 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
CG11175-RA 1..1542 390..1931 100   Plus
Sim4 to dmel-all-CDS-r6.02.fasta performed 2014-11-27 05:21:15 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
Rcd6-RA 1..1542 390..1931 100   Plus
Sim4 to dmel-all-transcript-r5.12.fasta performed 2008-11-11 01:11:40 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
CG11175-RA 1..2541 1..2541 100   Plus
Sim4 to dmel-all-transcript-r5.32.fasta performed 2011-03-16 20:57:31 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
Rcd6-RA 30..2570 1..2541 100   Plus
Sim4 to dmel-all-transcript-r5.52.fasta performed 2013-08-04 07:10:30 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
Rcd6-RA 34..2574 1..2541 100   Plus
Sim4 to dmel-all-transcript-r5.9.fasta performed 2008-07-21 21:40:30 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
CG11175-RA 1..2541 1..2541 100   Plus
Sim4 to dmel-all-transcript-r6.02.fasta performed 2014-11-27 05:21:15 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
Rcd6-RA 34..2574 1..2541 100   Plus
Sim4 to na_all.dmel.RELEASE6 performed 2019-03-16 03:59:29 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
2R 20633351..20633473 1..123 100   Minus
2R 20628186..20629932 795..2541 100 <- Minus
2R 20630026..20630265 555..794 100 <- Minus
2R 20630684..20631114 124..554 100 <- Minus
Sim4 to na_all.dmel.RELEASE6 performed 2019-03-16 03:59:29 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
2R 20633351..20633473 1..123 100   Minus
2R 20628186..20629932 795..2541 100 <- Minus
2R 20630026..20630265 555..794 100 <- Minus
2R 20630684..20631114 124..554 100 <- Minus
Sim4 to na_all.dmel.RELEASE6 performed 2019-03-16 03:59:29 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
2R 20633351..20633473 1..123 100   Minus
2R 20628186..20629932 795..2541 100 <- Minus
2R 20630026..20630265 555..794 100 <- Minus
2R 20630684..20631114 124..554 100 <- Minus
Sim4 to na_arms.dmel.RELEASE5 performed 2013-08-04 07:10:30 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
arm_2R 16515691..16517437 795..2541 100 <- Minus
arm_2R 16517531..16517770 555..794 100 <- Minus
arm_2R 16518189..16518619 124..554 100 <- Minus
arm_2R 16520856..16520978 1..123 100   Minus
Sim4 to na_arms.dmel.RELEASE6 performed 2011-12-09 18:23:36 Download gff for LD20239.complete
Subject Subject Range Query Range Percent Splice Strand
2R 20629385..20631131 795..2541 100 <- Minus
2R 20631225..20631464 555..794 100 <- Minus
2R 20631883..20632313 124..554 100 <- Minus
2R 20634550..20634672 1..123 100   Minus

LD20239.pep Sequence

Translation from 389 to 1930

> LD20239.pep
MNYQKASEKQSSSSLKKRPPGNGNSIQNFWNDRIMERFIKANLFIICCVV
AVLLLIVYLGAFSCEVSWILEAHGELPFAAYTLCSLYFVMFVATTILIHG
LVSGLCWPLFAWSGIIGLLSIPELVFVMIMTTQHWGLQSVHGLTELTSYL
IRLIINCFALICVIPTGIRWRRETQVLSQLQGLATRLSLQTPAPSVPITK
ADSRRSSQRLSGFENAGYQLCDETASKLPLGPGMGLGMNNQCGGSQAFGS
QNEFNASMFAPALAQQFNNATLMQRGGTGGAGGGHRAQSLMDLRCTLPGM
YNPRHVLDTEDKNAKYFNITIDDLKNNLHDSHRPSPPSLIGSTSNDPIYC
SIEPKQLTPPPAQQRSHHRPRGTHKQPPPGKLSRNCVSLENLDGISKVQN
DLTAYGNNLLQNYTQQQQYYLAMLLHQQQQQQLHHQQAGGIYRRPSNCSS
TGGFAGTVLAQPMQRRGSTHSQQMQYYGGFGYANYTNPYITANSKLSLGN
ESDDYRKYRDVAL*

LD20239.pep Blast Records

Blast to dana-all-translation-r1.3.fasta performed 2019-03-16 14:42:33
Subject Length Description Subject Range Query Range Score Percent Strand
Dana\GF12754-PA 508 GF12754-PA 1..508 1..513 2387 94 Plus
Blast to dere-all-translation-r1.3.fasta performed 2019-03-16 14:42:34
Subject Length Description Subject Range Query Range Score Percent Strand
Dere\GG20844-PA 513 GG20844-PA 1..513 1..513 2712 98.2 Plus
Blast to dgri-all-translation-r1.3.fasta performed 2019-03-16 14:42:35
Subject Length Description Subject Range Query Range Score Percent Strand
Dgri\GH19897-PA 503 GH19897-PA 1..503 1..513 2043 81 Plus
Blast to dmel-all-translation-r6.23.fasta performed 2019-03-25 11:09:45
Subject Length Description Subject Range Query Range Score Percent Strand
Rcd6-PB 513 CG11175-PB 1..513 1..513 2725 100 Plus
Rcd6-PA 513 CG11175-PA 1..513 1..513 2725 100 Plus
Blast to dmoj-all-translation-r1.3.fasta performed 2019-03-16 14:42:36
Subject Length Description Subject Range Query Range Score Percent Strand
Dmoj\GI19853-PA 519 GI19853-PA 1..519 1..513 1920 73.6 Plus
Blast to dper-all-translation-r1.3.fasta performed 2019-03-16 14:42:37
Subject Length Description Subject Range Query Range Score Percent Strand
Dper\GL17436-PA 524 GL17436-PA 1..524 1..513 2290 88 Plus
Blast to dpse-all-translation-r3.2.fasta performed 2019-03-16 14:42:38
Subject Length Description Subject Range Query Range Score Percent Strand
Dpse\GA10817-PA 524 GA10817-PA 1..524 1..513 2301 88.4 Plus
Blast to dsec-all-translation-r1.3.fasta performed 2019-03-16 14:42:39
Subject Length Description Subject Range Query Range Score Percent Strand
Dsec\GM19773-PA 513 GM19773-PA 1..513 1..513 2733 99 Plus
Blast to dsim-all-translation-r1.4.fasta performed 2019-03-16 14:42:40
Subject Length Description Subject Range Query Range Score Percent Strand
Dsim\GD25263-PA 513 GD25263-PA 1..513 1..513 2740 99.2 Plus
Blast to dvir-all-translation-r1.2.fasta performed 2019-03-16 14:42:41
Subject Length Description Subject Range Query Range Score Percent Strand
Dvir\GJ18850-PA 520 GJ18850-PA 1..520 1..513 2002 80 Plus
Blast to dwil-all-translation-r1.3.fasta performed 2019-03-16 14:42:42
Subject Length Description Subject Range Query Range Score Percent Strand
Dwil\GK21828-PA 504 GK21828-PA 1..504 1..513 2134 83.6 Plus
Blast to dyak-all-translation-r1.3.fasta performed 2019-03-16 14:42:43
Subject Length Description Subject Range Query Range Score Percent Strand
Dyak\GE13784-PA 514 GE13784-PA 1..514 1..513 2681 97.5 Plus

LD20239.hyp Sequence

Translation from 389 to 1930

> LD20239.hyp
MNYQKASEKQSSSSLKKRPPGNGNSIQNFWNDRIMERFIKANLFIICCVV
AVLLLIVYLGAFSCEVSWILEAHGELPFAAYTLCSLYFVMFVATTILIHG
LVSGLCWPLFAWSGIIGLLSIPELVFVMIMTTQHWGLQSVHGLTELTSYL
IRLIINCFALICVIPTGIRWRRETQVLSQLQGLATRLSLQTPAPSVPITK
ADSRRSSQRLSGFENAGYQLCDETASKLPLGPGMGLGMNNQCGGSQAFGS
QNEFNASMFAPALAQQFNNATLMQRGGTGGAGGGHRAQSLMDLRCTLPGM
YNPRHVLDTEDKNAKYFNITIDDLKNNLHDSHRPSPPSLIGSTSNDPIYC
SIEPKQLTPPPAQQRSHHRPRGTHKQPPPGKLSRNCVSLENLDGISKVQN
DLTAYGNNLLQNYTQQQQYYLAMLLHQQQQQQLHHQQAGGIYRRPSNCSS
TGGFAGTVLAQPMQRRGSTHSQQMQYYGGFGYANYTNPYITANSKLSLGN
ESDDYRKYRDVAL*

LD20239.hyp Blast Records

Blast to dmel-all-translation-r6.02.fasta performed 2014-11-28 14:03:24
Subject Length Description Subject Range Query Range Score Percent Strand
Rcd6-PB 513 CG11175-PB 1..513 1..513 2725 100 Plus
Rcd6-PA 513 CG11175-PA 1..513 1..513 2725 100 Plus