Clone RE54042 Report

Search the DGRC for RE54042

Clone and Library Details

Library:RE
Tissue Source:Drosophila melanogaster embryo
Created by:Piero Carninci, RIKEN Genome Science Laboratory
Date Registered:2000-10-23
Comments:Average reported size from P Carninci is 2.3kb. Directionally cloned:5 end at XhoI, 3 end at BamHI
Original Plate Number:540
Well:42
Vector:pFlc-1
Associated Gene/TranscriptmRpL39-RA
Protein status:RE54042.pep: gold
Sequenced Size:1133

Associated Genes

Associations are from manual ordering of a clone or by a periodic analysis.
Gene Date Evidence
mRpL39-RA 2011-07-22 Manual selection by Sue Celniker

Clone Sequence Records

RE54042.complete Sequence

1133 bp assembled on 2011-09-14

GenBank Submission: BT128888.1

> RE54042.complete
GTGAACTGCATCCCTGAAGAGTATTTTGGTAATTTACCATGTCTGCGGCC
ACCAAATTACATAAAACAAGCTGGTGCGCCCTGCGGCAGCTTCAACAATA
CAGAACTAAGGCCAACTTTAGTGGCAGTTCTGCATCGTTAGCCAAGCGGA
ATGACCTGTTCAACCAGGAGCAACGCCGTCAACGGGATGCAGTGGGTCGA
ATCGATAAGATCGAGGTGCGGTATCTGGGACTTCCCGAGGATGTCACTCT
GGTGATGAACGGCAACATCTCAACGCCCTTCAATTGCGCCCAGCATCTGA
GTGAGGGGCACTGTAAGCGATCGGCACTGGCCTTGATCGACGGCAGTGTT
CCCTGGGATATGCACAGACCCTTGCAGGAATCCTGTACTCTGCAGCTGCT
TAACTTCCATGTTTCCGAGCCACATGTGGTCAACAAAGCATTCTGGCGCA
CTTGCAGCTTTATGTTGGGAGCCGCCTTGAACCGCGCTTTCAAGCCGGAG
GCCAATCTTCAGCTCCACAGCTTTCCTGGACCCAATATCAAATCAGGTAG
CTTCGTACACGACATTGTGCTCCAAACCCAGAACTGGGAGCCAGGAAAAG
AAGAGATGCGCGCCCTTTCGGCAGAGATGGTTAAACTGGCTGCTCAGGAT
CTGCGCATCGAGCGTTTGGACGTCCAACAGGATCTGGCCCAGGAGATGTT
CAAGGATTCCAAGTATAAGAGCGAACAGTTGCCCAGCATCTCGCAGCAGA
CCAATGGAAGGGTCACCTTGTATCGCCTGGGTGATCATATCGACATCTCA
CGCGGTCCAATGGTGGCGTCTACCAGCTTTTTGGGGAAATGCGTCATCTC
GGCTGCCCACAAAGTTGCGGAGGAGGGTCCCTCTGGTGCTTTCTATCGCA
TTCAGGGCGTTGCACTGCCGTCTGGCTTCCAACTGAATCATGTTGCATTT
GGTGTATTGGAGGAGCGTTCTAAGAAACCTAGCCCCGCACGACTGCCCAA
TGAACCATTTGAGGAACAACAACAACTGCAATTATCTTAAAACGTTCTTT
AATATTTAAAACTATACTGTAAGTGTTAAAAAAGTAAATCATTAAAGAGC
GTCCTAATTTGTTATAACAAAAAAAAAAAAAAA

RE54042.complete Blast Records

Blast to d_melanogaster_OreR.fa performed 2019-03-15 11:01:12
Subject Length Description Subject Range Query Range Score Percent Strand
chr3L 24539361 chr3L 14988252..14988694 980..538 2200 99.8 Minus
chr3L 24539361 chr3L 14989033..14989358 436..111 1615 99.7 Minus
chr3L 24539361 chr3L 14988053..14988190 1118..981 690 100 Minus
chr3L 24539361 chr3L 14989609..14989719 111..1 555 100 Minus
chr3L 24539361 chr3L 14988868..14988968 537..437 505 100 Minus
Blast to na_all.dmel.RELEASE6 performed 2019-03-15 11:01:10
Subject Length Description Subject Range Query Range Score Percent Strand
3L 28110227 3L 14998180..14998622 980..538 2215 100 Minus
3L 28110227 3L 14998961..14999286 436..111 1615 99.7 Minus
3L 28110227 3L 14997973..14998118 1126..981 715 99.3 Minus
3L 28110227 3L 14999537..14999647 111..1 555 100 Minus
3L 28110227 3L 14998796..14998896 537..437 505 100 Minus
Blast to na_arms.dmel.RELEASE6 performed 2011-12-12 23:01:36
Subject Length Description Subject Range Query Range Score Percent Strand
3L 28103327 3L 14991280..14991722 980..538 2215 100 Minus
3L 28103327 3L 14992061..14992386 436..111 1615 99.6 Minus
3L 28103327 3L 14991073..14991218 1126..981 715 99.3 Minus
3L 28103327 3L 14992637..14992747 111..1 555 100 Minus
3L 28103327 3L 14991896..14991996 537..437 505 100 Minus
Blast to na_te.dros performed on 2019-03-15 11:01:11 has no hits.

RE54042.complete Sim4 Records

Sim4 to d_melanogaster_OreR.fa performed 2019-03-15 11:02:17 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
chr3L 14988053..14988190 981..1118 100 <- Minus
chr3L 14988252..14988694 538..980 99 <- Minus
chr3L 14988868..14988968 437..537 100 <- Minus
chr3L 14989033..14989357 112..436 99 <- Minus
chr3L 14989609..14989719 1..111 100   Minus
Sim4 to dmel-all-CDS-r5.32.fasta performed 2011-09-14 16:22:41 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
mRpL39-RA 1..1002 39..1040 99   Plus
Sim4 to dmel-all-CDS-r5.52.fasta performed 2013-08-03 21:33:14 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
mRpL39-RA 1..1002 39..1040 99   Plus
Sim4 to dmel-all-CDS-r6.02.fasta performed 2014-11-26 17:19:30 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
mRpL39-RA 1..1002 39..1040 99   Plus
Sim4 to dmel-all-transcript-r5.32.fasta performed 2011-09-14 16:22:41 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
mRpL39-RA 18..1135 1..1118 99   Plus
Sim4 to dmel-all-transcript-r5.52.fasta performed 2013-08-03 21:33:14 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
mRpL39-RA 20..1137 1..1118 99   Plus
Sim4 to dmel-all-transcript-r6.02.fasta performed 2014-11-26 17:19:30 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
mRpL39-RA 20..1137 1..1118 99   Plus
Sim4 to na_all.dmel.RELEASE6 performed 2019-03-15 11:02:17 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
3L 14997981..14998118 981..1118 100 <- Minus
3L 14998180..14998622 538..980 100 <- Minus
3L 14998796..14998896 437..537 100 <- Minus
3L 14998961..14999285 112..436 99 <- Minus
3L 14999537..14999647 1..111 100   Minus
Sim4 to na_all.dmel.RELEASE6 performed 2019-03-15 11:02:17 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
3L 14997981..14998118 981..1118 100 <- Minus
3L 14998180..14998622 538..980 100 <- Minus
3L 14998796..14998896 437..537 100 <- Minus
3L 14998961..14999285 112..436 99 <- Minus
3L 14999537..14999647 1..111 100   Minus
Sim4 to na_all.dmel.RELEASE6 performed 2019-03-15 11:02:17 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
3L 14997981..14998118 981..1118 100 <- Minus
3L 14998180..14998622 538..980 100 <- Minus
3L 14998796..14998896 437..537 100 <- Minus
3L 14998961..14999285 112..436 99 <- Minus
3L 14999537..14999647 1..111 100   Minus
Sim4 to na_arms.dmel.RELEASE5 performed 2013-08-03 21:33:14 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
arm_3L 14991081..14991218 981..1118 100 <- Minus
arm_3L 14991280..14991722 538..980 100 <- Minus
arm_3L 14991896..14991996 437..537 100 <- Minus
arm_3L 14992061..14992385 112..436 99 <- Minus
arm_3L 14992637..14992747 1..111 100   Minus
Sim4 to na_arms.dmel.RELEASE6 performed 2011-12-09 19:48:20 Download gff for RE54042.complete
Subject Subject Range Query Range Percent Splice Strand
3L 14991280..14991722 538..980 100 <- Minus
3L 14991896..14991996 437..537 100 <- Minus
3L 14992061..14992385 112..436 99 <- Minus
3L 14992637..14992747 1..111 100   Minus
3L 14991081..14991218 981..1118 100 <- Minus

RE54042.pep Sequence

Translation from 38 to 1039

> RE54042.pep
MSAATKLHKTSWCALRQLQQYRTKANFSGSSASLAKRNDLFNQEQRRQRD
AVGRIDKIEVRYLGLPEDVTLVMNGNISTPFNCAQHLSEGHCKRSALALI
DGSVPWDMHRPLQESCTLQLLNFHVSEPHVVNKAFWRTCSFMLGAALNRA
FKPEANLQLHSFPGPNIKSGSFVHDIVLQTQNWEPGKEEMRALSAEMVKL
AAQDLRIERLDVQQDLAQEMFKDSKYKSEQLPSISQQTNGRVTLYRLGDH
IDISRGPMVASTSFLGKCVISAAHKVAEEGPSGAFYRIQGVALPSGFQLN
HVAFGVLEERSKKPSPARLPNEPFEEQQQLQLS*

RE54042.pep Blast Records

Blast to dana-all-translation-r1.3.fasta performed 2019-03-16 19:33:37
Subject Length Description Subject Range Query Range Score Percent Strand
Dana\GF10636-PA 333 GF10636-PA 1..333 1..333 1611 88.6 Plus
Dana\GF21565-PA 749 GF21565-PA 128..336 78..299 227 29.8 Plus
Blast to dere-all-translation-r1.3.fasta performed 2019-03-16 19:33:38
Subject Length Description Subject Range Query Range Score Percent Strand
Dere\GG13700-PA 333 GG13700-PA 1..333 1..333 1745 96.7 Plus
Dere\GG23767-PA 746 GG23767-PA 125..333 78..299 228 28.6 Plus
Blast to dgri-all-translation-r1.3.fasta performed 2019-03-16 19:33:38
Subject Length Description Subject Range Query Range Score Percent Strand
Dgri\GH14833-PA 332 GH14833-PA 1..332 1..333 1431 78.1 Plus
Blast to dmel-all-translation-r6.23.fasta performed 2019-03-25 11:19:14
Subject Length Description Subject Range Query Range Score Percent Strand
mRpL39-PA 333 CG17166-PA 1..333 1..333 1728 100 Plus
Blast to dmoj-all-translation-r1.3.fasta performed 2019-03-16 19:33:39
Subject Length Description Subject Range Query Range Score Percent Strand
Dmoj\GI13938-PA 332 GI13938-PA 1..332 1..333 1426 79.6 Plus
Dmoj\GI17149-PA 691 GI17149-PA 70..278 78..299 225 29.8 Plus
Blast to dper-all-translation-r1.3.fasta performed 2019-03-16 19:33:39
Subject Length Description Subject Range Query Range Score Percent Strand
Dper\GL25954-PA 334 GL25954-PA 4..334 3..333 1587 86.4 Plus
Dper\GL19239-PA 754 GL19239-PA 133..341 78..299 233 30.2 Plus
Blast to dpse-all-translation-r3.2.fasta performed 2019-03-16 19:33:40
Subject Length Description Subject Range Query Range Score Percent Strand
Dpse\GA14359-PA 334 GA14359-PA 4..334 3..333 1587 86.4 Plus
Dpse\GA18821-PB 754 GA18821-PB 133..341 78..299 233 30.2 Plus
Blast to dsec-all-translation-r1.3.fasta performed 2019-03-16 19:33:40
Subject Length Description Subject Range Query Range Score Percent Strand
Dsec\GM24519-PA 333 GM24519-PA 1..333 1..333 1783 99.1 Plus
Dsec\GM26732-PA 747 GM26732-PA 126..334 78..299 228 28.6 Plus
Blast to dsim-all-translation-r1.4.fasta performed 2019-03-16 19:33:41
Subject Length Description Subject Range Query Range Score Percent Strand
Dsim\GD12590-PA 333 GD12590-PA 1..333 1..333 1783 99.1 Plus
Dsim\GD17572-PA 144 GD17572-PA 1..144 190..333 755 99.3 Plus
Dsim\GD23818-PA 747 GD23818-PA 126..334 78..299 228 28.6 Plus
Blast to dvir-all-translation-r1.2.fasta performed 2019-03-16 19:33:41
Subject Length Description Subject Range Query Range Score Percent Strand
Dvir\GJ13727-PA 332 GJ13727-PA 1..332 1..333 1464 80.5 Plus
Dvir\GJ17652-PA 745 GJ17652-PA 124..332 78..299 223 29.3 Plus
Blast to dwil-all-translation-r1.3.fasta performed 2019-03-16 19:33:42
Subject Length Description Subject Range Query Range Score Percent Strand
Dwil\GK10572-PA 331 GK10572-PA 1..331 1..333 1447 77.2 Plus
Dwil\GK21088-PA 699 GK21088-PA 78..286 78..299 219 28.6 Plus
Blast to dyak-all-translation-r1.3.fasta performed 2019-03-16 19:33:43
Subject Length Description Subject Range Query Range Score Percent Strand
Dyak\GE19994-PA 333 GE19994-PA 1..333 1..333 1750 97 Plus
Dyak\Aats-thr-PA 747 GE18572-PA 126..334 78..299 226 28.6 Plus

RE54042.hyp Sequence

Translation from 38 to 1039

> RE54042.hyp
MSAATKLHKTSWCALRQLQQYRTKANFSGSSASLAKRNDLFNQEQRRQRD
AVGRIDKIEVRYLGLPEDVTLVMNGNISTPFNCAQHLSEGHCKRSALALI
DGSVPWDMHRPLQESCTLQLLNFHVSEPHVVNKAFWRTCSFMLGAALNRA
FKPEANLQLHSFPGPNIKSGSFVHDIVLQTQNWEPGKEEMRALSAEMVKL
AAQDLRIERLDVQQDLAQEMFKDSKYKSEQLPSISQQTNGRVTLYRLGDH
IDISRGPMVASTSFLGKCVISAAHKVAEEGPSGAFYRIQGVALPSGFQLN
HVAFGVLEERSKKPSPARLPNEPFEEQQQLQLS*

RE54042.hyp Blast Records

Blast to dmel-all-translation-r6.02.fasta performed 2014-11-28 17:23:09
Subject Length Description Subject Range Query Range Score Percent Strand
mRpL39-PA 333 CG17166-PA 1..333 1..333 1728 100 Plus