RetrogeneDB ID: retro_btau_1406

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:111053282..111053782(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX4I1
• Ensembl ID: ENSBTAG00000016079
• Aliases: COX4I1, COX4
• Description: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P00423]

Sequence

>retro_btau_1406
ATATTGGCGACAAGAGTATTTAGCCTGATTGGCAGGCGTGCAGTTTCCACCTCGGTGTGTGTTCGGGCCCATGGAAGTGT
TGTAAAGAGTGAAGATTATGCTCTCCCGAGTTATGTGGACCGGCGTGACTACCCCTTGCCCGACGTGGCCCACGTCAAGA
ACCTGTCTGCCAGCCAGAAGGCCTTGAAGCAGAAGGAGAAGGCTTCCTGGAGCAGCCTCTCCATCGGTGAGAAAGTTGAA
CTGCACGACCTTAAGTTCAAGGAGAGCTTCGCTGAGATGCGCAGGAGCACAACAGGTGCCAGACAGTGGTGGGCGCGGCC
ACGTTCTTCATCGGCTTCACCGCGCTCCTCACCTGGGAGAAGCGCTGTGTGTACGGCCCCATCCTGCACACCTTTGAAGA
GGAGTGGGTGGCCAAGCAGACCAGGAGGATGCTCGACGTGAAGGTGGCCCCCATCCAGGGCTTCTCAGCCAAGCGGGACT
ACGACAAGAACAAGTGGAAG

Alignment

ORF - retro_btau_1406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLATRVFSLIGRRAISTSVCVRAHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASW
          .LATRVFSLIGRRA.STSVCVRAHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALK.KEKASW
Retrocopy ILATRVFSLIGRRAVSTSVCVRAHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKQKEKASW

Parental  SSLSIDEKVELYRLKFKESFAEMNRST-NEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVA
          SSLSI.EKVEL..LKFKESFAEM.RST.N...TVVGAA.FFIGFTA.LL.WEK..VYGPI.HTFEEEWVA
Retrocopy SSLSIGEKVELHDLKFKESFAEMRRST<NRCQTVVGAATFFIGFTA-LLTWEKRCVYGPILHTFEEEWVA

Parental  KQTKRMLDMKVAPIQGFSAKWDYDKNEWK
          KQT.RMLD.KVAPIQGFSAK.DYDKN.WK
Retrocopy KQTRRMLDVKVAPIQGFSAKRDYDKNKWK

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
ERP005899_liver	0.00 RPM	30.42 RPM
ERP005899_muscle	0.48 RPM	551.22 RPM
SRP017611_brain	0.00 RPM	131.78 RPM
SRP017611_kidney	0.00 RPM	203.42 RPM
SRP017611_liver	0.00 RPM	81.10 RPM
SRP030211_testis	0.13 RPM	238.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1406 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1406 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,