RetrogeneDB ID: retro_mmus_2958

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:100624517..100624958(+)
• Located in intron of: ENSMUSG00000030704

Retrocopy information

• Ensembl ID: ENSMUSG00000082210
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cox4i1
• Ensembl ID: ENSMUSG00000031818
• Aliases: Cox4i1, AL024441, COXIV, Cox4, Cox4a
• Description: cytochrome c oxidase subunit IV isoform 1 [Source:MGI Symbol;Acc:MGI:88473]

Sequence

>retro_mmus_2958
ATGATGGCTACCAGAGCACTTAGCTTAATTGGCAAGAGAGCCATTTCTACTTCGGTATATGTCCTGATCACACGGGAGTG
TTATAAAGAGTGAAGACTATGCTCTCCCTGGTTGTGTTGATATGCATGACCACCCATGCCTGGTGTGGCCCATGTCAGGC
TGCTGTCTGCCAGCTAGAAAGCCCTGAAGGAGAAGGCTGGCCTGCAGCAGCCTGTCCAGCCATGACAAAGTCCAATTGTA
CTGCATCCAGTTTAACAAGAGCTTTGCTAAGATGAACAGGAGCACCAATGAGTGGAAAACTCTTGTGGGCGTGGCCATGT
TTTTCATGGGATTCATGCTCTAATTCTGATGTGGGAGAAACACCATGGGTACAGCCCCATCCCTCATAGCTTTGATGGAG
ACTGGGTGGCTATGCAAAGCCAGCAGATGCTGGACAAGAAG

Alignment

ORF - retro_mmus_2958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.32 %
• Parental protein coverage: 88.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLASRALSLIGKRAISTSVCLR-AHGSVVKSEDYAFPTYADRRDYP-LPDVAHVTMLSASQKALKEKEKA
          M.A.RALSLIGKRAISTSV.....HGSV.KSEDYA.P...D..D.P..P.VAHV..LSAS.KALK..EKA
Retrocopy MMATRALSLIGKRAISTSVYVL>SHGSVIKSEDYALPGCVDMHDHP<MPGVAHVRLLSAS*KALK--EKA

Parental  DW-SSLSRDEKVQLYRIQFNESFAEMNRGTNEWKTVVGMAMFFIGFT-ALVLIWEKSYVYGPIPHTFDRD
          ...SSLS...KVQLY.IQFN.SFA.MNR.TNEWKT.VG.AMFF.GF..AL.L.WEK...Y.PIPH.FD.D
Retrocopy GL>SSLSSHDKVQLYCIQFNKSFAKMNRSTNEWKTLVGVAMFFMGFM<ALILMWEKHHGYSPIPHSFDGD

Parental  WVAMQTKRMLDMK
          WVAMQ...MLD.K
Retrocopy WVAMQSQQMLDKK

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	0.07 RPM	287.39 RPM
SRP007412_cerebellum	0.04 RPM	312.11 RPM
SRP007412_heart	0.00 RPM	988.32 RPM
SRP007412_kidney	0.02 RPM	664.69 RPM
SRP007412_liver	0.00 RPM	237.53 RPM
SRP007412_testis	0.00 RPM	149.57 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2958 was not detected

EST

No EST(s) were mapped for retro_mmus_2958 retrocopy.

TSS

No TSS is located nearby retro_mmus_2958 retrocopy 5' end.

Lab

retro_mmus_2958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2958 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005479	1 retrocopy	retro_acar_90,
Ailuropoda melanoleuca	ENSAMEG00000018274	1 retrocopy	retro_amel_470,
Bos taurus	ENSBTAG00000016079	2 retrocopies	retro_btau_1406, retro_btau_483,
Canis familiaris	ENSCAFG00000019921	2 retrocopies	retro_cfam_1259, retro_cfam_1906,
Callithrix jacchus	ENSCJAG00000017319	4 retrocopies	retro_cjac_2267, retro_cjac_3264, retro_cjac_3300, retro_cjac_802,
Dasypus novemcinctus	ENSDNOG00000017207	3 retrocopies	retro_dnov_2207, retro_dnov_2396, retro_dnov_737,
Equus caballus	ENSECAG00000011722	1 retrocopy	retro_ecab_418,
Felis catus	ENSFCAG00000007612	2 retrocopies	retro_fcat_1484, retro_fcat_853,
Homo sapiens	ENSG00000131143	1 retrocopy	retro_hsap_1428,
Gorilla gorilla	ENSGGOG00000010047	1 retrocopy	retro_ggor_1101,
Loxodonta africana	ENSLAFG00000014002	1 retrocopy	retro_lafr_528,
Macaca mulatta	ENSMMUG00000006763	4 retrocopies	retro_mmul_1129, retro_mmul_1285, retro_mmul_1724, retro_mmul_2260,
Mus musculus	ENSMUSG00000031818	2 retrocopies	retro_mmus_1305, retro_mmus_2958 ,
Nomascus leucogenys	ENSNLEG00000011409	1 retrocopy	retro_nleu_1843,
Oryctolagus cuniculus	ENSOCUG00000001735	5 retrocopies	retro_ocun_1238, retro_ocun_1333, retro_ocun_317, retro_ocun_469, retro_ocun_889,
Ochotona princeps	ENSOPRG00000002129	4 retrocopies	retro_opri_1205, retro_opri_267, retro_opri_821, retro_opri_857,
Pongo abelii	ENSPPYG00000007619	3 retrocopies	retro_pabe_1183, retro_pabe_1184, retro_pabe_996,
Pan troglodytes	ENSPTRG00000008434	1 retrocopy	retro_ptro_977,
Rattus norvegicus	ENSRNOG00000017817	1 retrocopy	retro_rnor_1157,
Tarsius syrichta	ENSTSYG00000009682	2 retrocopies	retro_tsyr_2073, retro_tsyr_591,