RetrogeneDB ID: retro_mmus_2989

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:7096848..7098028(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Actr2
• Ensembl ID: ENSMUSG00000020152
• Aliases: Actr2, 4921510D23Rik, AA409782, Arp2, D6Ertd746e
• Description: ARP2 actin-related protein 2 [Source:MGI Symbol;Acc:MGI:1913963]

Sequence

>retro_mmus_2989
ATGGACAGCCAGGGCAGGAAGGTGGTGGTGTGCGACAATGGCACTGGATTTGTGAAGTGTGGATATGCAGGCTCTAACTT
TCCAGAACACATCTTCCCAGCTTTGGTTGTAAGACCTATTATCAGATCAACCACCAAAGGGGGAAACATTGAAATCAAGG
ACCTTATGGTTGGTGATGAGGCAAGTAAGCTGTGTTCCATGTTGGAAGTGAACTACCCTATGGAGAATGGCATCGTGCAG
AATTGGGATGACATGAAGCCCCTGTAGGACTACACATTTGGACCAGAGAAACTCAATATAGACACCAGAAACTGCAAGAT
TTTACTTACAGGACCATCTATGAATCCAACCAAAAACAGAGAGAAGATTGTAAAGGTAATGTTTGAAACTTACCAGATTT
CTGGTGTGTATGTAGCCATCCAGGCAGTTCTGACTTTGTATGCTCAATGTTTACTGACTGGTGTAGTAGTGAACTCTGGA
GATGGTGTCACTTACATTTGCCCAGTATATGAAGGCTTTTCTCTCCCTCACCTTACAAGGAGGCTGGATATGACTGGGAG
GGATATTACCAGGTATCTTATCAAGCTGCTGCTGTTGCAAGGATATGCCTTCAACCATTCTGCTGATTTTGAGACAGTTT
TCATGATTAAAGAAAACTTTGTTATGTGGGTTACAATATTGAGCAAGAGCAGAAGCTAGCCGTAGAGACCACAGTGTTAG
TTGAGTCATATACACTTCCAGATGGACATATTATTAAGGTTGGAGGAGAAAGATTTGAACACCAGAAACTTTATTTCAGC
CTTATTTGATCAATGTTGAGGGGGTTGGTATTGCTTAATTGCTTTTTAACACAATCCAAGCAGCCGACATTGATACCAGA
TCTGAATTTTACAAGCCCATTGTGCTTTCTGGAGGTTCTACCATGTATTCTGGCCTGCCATGATCGAGGTTGAACAAGAA
CTTAAACAGCTTTACTTAGAACGAGTTCTGAAAGAAGGTGTGGAAAAACTTTCAAAATTTAAGATCCAAATTGAAGACCC
ACCCCGCAGGAAGCACGTGGTGTTCTTGAGTGGCACATATCCTAGCAGACCTCATGACATACAAAAACAACTTTTGGATG
ACCAGACAAGAGTACCAAGAAAACGGTGTCTGCGTGCTGGAGAAAGTCGATGTAACTGTT

Alignment

ORF - retro_mmus_2989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDEASELRSMLEV
          MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALV.RPIIRSTTK.GNIEIKDLMVGDEAS.L.SMLEV
Retrocopy MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVVRPIIRSTTKGGNIEIKDLMVGDEASKLCSMLEV

Parental  NYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNREKIVEVMFETYQFSGVYVAI
          NYPMENGIV.NWDDMK.L.DYTFGPEKLNIDTRNCKILLT.P.MNPTKNREKIV.VMFETYQ.SGVYVAI
Retrocopy NYPMENGIVQNWDDMKPL*DYTFGPEKLNIDTRNCKILLTGPSMNPTKNREKIVKVMFETYQISGVYVAI

Parental  QAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLLRGYAFNHSADF
          QAVLTLYAQ.LLTGVVV.SGDGVT.ICPVYEGFSLPHLTRRLD..GRDITRYLIKLLLL.GYAFNHSADF
Retrocopy QAVLTLYAQCLLTGVVVNSGDGVTYICPVYEGFSLPHLTRRLDMTGRDITRYLIKLLLLQGYAFNHSADF

Parental  ETVRMIKE-KLCYVGYNIEQEQKLALETTVLVESYTLPDGRIIKVGGERFE-APEALFQPHLINVEGVGV
          ETV.MIKE.KLCYVGYNIEQEQKLA.ETTVLVESYTLPDG.IIKVGGERFE..PE.LFQP.LINVEGVG.
Retrocopy ETVFMIKE<KLCYVGYNIEQEQKLAVETTVLVESYTLPDGHIIKVGGERFE<TPETLFQPYLINVEGVGI

Parental  AELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLP-SRL-ERELKQLYLERVLKGDVEKLSKFKIRIED
          A.LLFNTIQAADIDTRSEFYK.IVLSGGSTMY.GLP.SRL.E.ELKQLYLERVLK..VEKLSKFKI.IED
Retrocopy A*LLFNTIQAADIDTRSEFYKPIVLSGGSTMYSGLP*SRL<EQELKQLYLERVLKEGVEKLSKFKIQIED

Parental  PPRRKHMVFLGGA-VLADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTV
          PPRRKH.VFL.G...LAD.M..K.NFWMTRQEYQE.GV.VLEK..VTV
Retrocopy PPRRKHVVFLSGT>ILADLMTYKNNFWMTRQEYQENGVCVLEKVDVTV

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	0.00 RPM	260.92 RPM
SRP007412_cerebellum	0.09 RPM	142.64 RPM
SRP007412_heart	0.03 RPM	65.65 RPM
SRP007412_kidney	0.08 RPM	152.82 RPM
SRP007412_liver	0.00 RPM	108.85 RPM
SRP007412_testis	0.18 RPM	36.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2989 was not detected

EST

No EST(s) were mapped for retro_mmus_2989 retrocopy.

TSS

No TSS is located nearby retro_mmus_2989 retrocopy 5' end.

Lab

retro_mmus_2989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2989 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009761	1 retrocopy	retro_btau_707,
Callithrix jacchus	ENSCJAG00000006722	1 retrocopy	retro_cjac_429,
Homo sapiens	ENSG00000138071	1 retrocopy	retro_hsap_1978,
Gorilla gorilla	ENSGGOG00000008505	1 retrocopy	retro_ggor_1435,
Monodelphis domestica	ENSMODG00000003364	2 retrocopies	retro_mdom_1082, retro_mdom_754,
Mus musculus	ENSMUSG00000020152	1 retrocopy	retro_mmus_2989 ,
Pongo abelii	ENSPPYG00000012359	1 retrocopy	retro_pabe_1877,
Pan troglodytes	ENSPTRG00000011990	1 retrocopy	retro_ptro_1320,