RetrogeneDB ID: retro_mmus_1973

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:130880865..130882130(+)
• Located in intron of: ENSMUSG00000085566

Retrocopy information

• Ensembl ID: ENSMUSG00000080989
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psmd11
• Ensembl ID: ENSMUSG00000017428
• Aliases: Psmd11, 1700089D09Rik, 1810019E17Rik, 2610024G20Rik, 2810055C24Rik, C78232, P44.5, S9
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 [Source:MGI Symbol;Acc:MGI:1916327]

Sequence

>retro_mmus_1973
ATGGCGGCCGCAGCGGTGGTGGAGTTCCAGAGAGTCCAGTCTCTACTTAGCACCGACCGGGAGGCCTCCATCGACATCCT
CCACTCCATCGTGAAACATGACAATCAAGAAAATGATGAGGAGGCAGTCCAGGTCAAAGAGCAGAGCATCCTTGAACTGG
GTTCTCTCCTGGCGAAGACTGGACAAGCTGATGAGCTTGGAGGACTCCTGAAGTATGTACGACCTTTCTTGAATTCCATC
AGTAAACTAAAGCAGCTCGTCTGGTCCGGTCTCTTCTTGATCTGTTTCTAGATATGGAAGCAGCTACAGGGCAGGAGGTC
GAGCTATGTTTAGAGTGCATCGAATGGGCCAAATCAGAGAAAAGAACTTTCTTACGCCAAGCATTGGAGGCAAGGCTGGT
GTCTTTGTATTTTGATACCAAGAGGTACCAGGAAGCATTGCATTTGGGTTCTCAGCTGCTTCGGGAGTTGAAAAAGATGG
ATGATAAAGCCCTTTTGGTGGAAGTACAGCTTTTAGAAAGCAAAACTTACCATGCTCTGAGTAATCTGCTGAAAGCCCGA
GCTGCCTTAACCTCTGCTCGAACCACAGCAAATGCCATCTACTGTCCCCCTAAATTGCAGGCCACCCTGGACATGCAGTC
AGGTATTATTCATGCAGCAGAGGAGAAGGACTGGAAAACTGCATACTCATACTTCTATGAGGCATTCGAAGGCTACGACT
CCATTGATAGCCCCAAGGCCATCACATCTCTGAAGTAGATGTTGCTGTGCAGAATCATGCTCAACACCCCAGAAGATGTC
CAGGCTTTGGTGAGCAGAAAGCTTGCACTTCGGTGTGCAGGGAGGCAGACAGAAGCATTGAAATGTGTGGCTCAAGCTAG
CAAGAACAGATCACTGGCAGATTTTGAAAAGGCCCTGACAGACTACAGGGCAGAGCTCCGGGACGACCCAATCATCAGCA
CACATTTGGCCAAGTTGTACAATAACTTACAGGAACAGAATCTGATCCGGGTTATTGAGTCTTTTTCCCGAGTCCAGATT
GAACACATATCTAGCCTCATCAAACTCTCCAAGGCCGACGTGGAGAGAAAATTATCACAGATGATTCTTGACAAAAAGTT
TCATGGGATTTTGGACCAGGGGGAGGGTGTCCTGATCATTTTCGATGAACCCCTAGTAGATAAAACTTATGAAGCTGCTC
TGGAAACTATTCAGAACAGGAGTAAAGTAGTGGACTCCCTCTACAGCAAAGCCAAGAAGCTGACA

Alignment

ORF - retro_mmus_1973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAAVVEFQRAQSLLSTDREASIDILHSIVKRDIQENDEEAVQVKEQSILELGSLLAKTGQAAELGGLL
          MAAAAVVEFQR.QSLLSTDREASIDILHSIVK.D.QENDEEAVQVKEQSILELGSLLAKTGQA.ELGGLL
Retrocopy MAAAAVVEFQRVQSLLSTDREASIDILHSIVKHDNQENDEEAVQVKEQSILELGSLLAKTGQADELGGLL

Parental  KYVRPFLNSISK-AKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSEKRTFLRQALEARLVSLYFD
          KYVRPFLNSISK..KAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSEKRTFLRQALEARLVSLYFD
Retrocopy KYVRPFLNSISK<TKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSEKRTFLRQALEARLVSLYFD

Parental  TKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKLQAT
          TKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHALSNL.KARAALTSARTTANAIYCPPKLQAT
Retrocopy TKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHALSNLLKARAALTSARTTANAIYCPPKLQAT

Parental  LDMQSGIIHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRY
          LDMQSGIIHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLK.MLLC.IMLNTPEDVQALVS.KLALR.
Retrocopy LDMQSGIIHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLK*MLLCRIMLNTPEDVQALVSRKLALRC

Parental  AGRQTEALKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEH
          AGRQTEALKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLY.NL.EQNLIRVIE.FSRVQIEH
Retrocopy AGRQTEALKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLYNNLQEQNLIRVIESFSRVQIEH

Parental  ISSLIKLSKADVERKLSQMILDKKFHGILDQGEGVLIIFDEPPVDKTYEAALETIQNMSKVVDSLYSKAK
          ISSLIKLSKADVERKLSQMILDKKFHGILDQGEGVLIIFDEP.VDKTYEAALETIQN.SKVVDSLYSKAK
Retrocopy ISSLIKLSKADVERKLSQMILDKKFHGILDQGEGVLIIFDEPLVDKTYEAALETIQNRSKVVDSLYSKAK

Parental  KLT
          KLT
Retrocopy KLT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	1.57 RPM	56.63 RPM
SRP007412_cerebellum	0.96 RPM	56.19 RPM
SRP007412_heart	0.97 RPM	53.82 RPM
SRP007412_kidney	1.66 RPM	58.85 RPM
SRP007412_liver	1.67 RPM	61.72 RPM
SRP007412_testis	1.14 RPM	50.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1973 was not detected

EST

1 EST(s) were mapped to retro_mmus_1973 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE457074	130880868	130881429	99.9	560	1	559

TSS

No TSS is located nearby retro_mmus_1973 retrocopy 5' end.

Lab

retro_mmus_1973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1973 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014450	1 retrocopy	retro_cjac_4166,
Mus musculus	ENSMUSG00000017428	1 retrocopy	retro_mmus_1973 ,
Tupaia belangeri	ENSTBEG00000001962	1 retrocopy	retro_tbel_1610,