RetrogeneDB ID: retro_mmus_3653

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:81821475..81822730(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082319
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Actr3
• Ensembl ID: ENSMUSG00000026341
• Aliases: Actr3, 1200003A09Rik, Arp3
• Description: ARP3 actin-related protein 3 [Source:MGI Symbol;Acc:MGI:1921367]

Sequence

>retro_mmus_3653
ATGGCGGGACGGCTGCCGGCCTGTGTGGTGGACTGTGGCACGGGATATACAAAACTAGGATATGCTGGAAATACAGAGCC
ACAGTTTATCATCCCATCATGTATTGCCATTAAAGAGTCTGCAAAAGTGGGTGACCAAGCCCAGAGGAGGGTGATGAAAG
GCGTGGATGACCTAGACTTCTTCATTGGTGATGAAACAATAGAAAAGCCCACATATGCAACAAAGTGGCCAATTCGCCAT
GGTATAGTTGAAGACTGGGACTTAATGGAAAGGTTTATGGAGCAAGTGATTTTTAAATATTTAAGGGCAGAACCTGAAGA
TCATTACTTTCTTTTGACTGAACCTCCACTGAATACTCCAGAAAACAGGGAATATACTGCTGAAATAATGTTTGAGTCCT
TCAATGTTCCAGGCTTGTACATTGCTGTGCAGGCTGTTCTTGCCTTAGCTGCATCCTGGACCTCAAGACAAGTAGGAGAG
CGGACGCTGACGGATACAGTAATAGACAGTGGAGACGGAGTCACTCATGTCATTCCTGTGGCTGAAGGATATGTTATCAG
CAGCTGTATTAAACACATTCCAATCGCAGGAAGAGATATAACATATTTTATTCAGCAACTGCTGCGAGACTGAGAAGTAG
GAATTCCTCCTGAGCAGTCCTTGGAAACTGCGAAAGCAGTGAAGGAACGCTACAGTTATGTCTGCCCAGATTTAGTAAAA
GAGTTTAACAAGTATGACACCAATGGGTCAAAGTGGATCGAACAGTACACCGGAGTCAACGCCATCTCAAAGAAAGAGTT
TTCTATTGATGTTGGCTATGAGCGATTCCTGGGACCCGAGATCTTTTTCCATCCAGAGTTTGCTAATCCAGATTTTACAA
CAACCTATCTCAGAAGATGTAGATGAAGTCATTCAGAATTGCCCCATTGATGTCTGGTGTCCTCTCTACAAGAACATTGT
CCTCTCTGGTGGTTCAACTATGTTCAGGGACTTTGGACATCGTTTGCAAAGAGATTTGAAGAGAACTGTAGATGCCAGGC
TGAAGTTAAGCGAGGAGCTGAGTGGTGGTAGATTGAAGCCCAAGCCTATTGATGTACAAGTTATTACACACCATATGCAG
TGGTATGCAGTCTGGTTTGGAGGGTCAATGCTGGCTTCCACGCCTGAGTTCTACCAAGTATGCCACACCAAAAAGGATTA
TGAAGAAATTGGACCTAGCATTTGTCGTCACAATCCAGTGTTTGGAGTCATGTCC

Alignment

ORF - retro_mmus_3653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP
          MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDE.IEKP
Retrocopy MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDETIEKP

Parental  TYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLY
          TYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLY
Retrocopy TYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLY

Parental  IAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRD
          IAVQAVLALAASWTSRQVGERTLT.TVIDSGDGVTHVIPVAEGYVI.SCIKHIPIAGRDITYFIQQLLRD
Retrocopy IAVQAVLALAASWTSRQVGERTLTDTVIDSGDGVTHVIPVAEGYVISSCIKHIPIAGRDITYFIQQLLRD

Parental  REVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGVNAISKKEFSIDVGYERFLGPE
          .EVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDT.GSKWI.QYTGVNAISKKEFSIDVGYERFLGPE
Retrocopy *EVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTNGSKWIEQYTGVNAISKKEFSIDVGYERFLGPE

Parental  IFFHPEFANPDFT-QPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKL
          IFFHPEFANPDFT.QPISE.VDEVIQNCPIDV..PLYKNIVLSGGSTMFRDFG.RLQRDLKRTVDARLKL
Retrocopy IFFHPEFANPDFT>QPISEDVDEVIQNCPIDVWCPLYKNIVLSGGSTMFRDFGHRLQRDLKRTVDARLKL

Parental  SEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
          SEELSGGRLKPKPIDVQVITHHMQ.YAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
Retrocopy SEELSGGRLKPKPIDVQVITHHMQWYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

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	0.72 RPM	101.93 RPM
SRP007412_cerebellum	0.56 RPM	57.06 RPM
SRP007412_heart	0.44 RPM	53.45 RPM
SRP007412_kidney	0.81 RPM	72.30 RPM
SRP007412_liver	0.27 RPM	43.64 RPM
SRP007412_testis	0.09 RPM	14.45 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3653 was not detected

EST

No EST(s) were mapped for retro_mmus_3653 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_158274	576 libraries	231 libraries	233 libraries	21 libraries	11 libraries
TSS #2	TSS_158275	401 libraries	513 libraries	155 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_3653 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3653 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003401	1 retrocopy	retro_btau_672,
Callithrix jacchus	ENSCJAG00000014091	4 retrocopies	retro_cjac_3602, retro_cjac_3813, retro_cjac_385, retro_cjac_4005,
Homo sapiens	ENSG00000115091	2 retrocopies	retro_hsap_1391, retro_hsap_4694,
Gorilla gorilla	ENSGGOG00000011346	1 retrocopy	retro_ggor_2921,
Mustela putorius furo	ENSMPUG00000010717	1 retrocopy	retro_mputfur_1275,
Mus musculus	ENSMUSG00000026341	1 retrocopy	retro_mmus_3653 ,
Nomascus leucogenys	ENSNLEG00000011619	2 retrocopies	retro_nleu_1077, retro_nleu_2364,
Pongo abelii	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468,