RetrogeneDB ID: retro_btau_1425

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:53209414..53210355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX10
• Ensembl ID: ENSBTAG00000015294
• Aliases: None
• Description: protoheme IX farnesyltransferase, mitochondrial [Source:RefSeq peptide;Acc:NP_001091482]

Sequence

>retro_btau_1425
ATGGCCGCATCCCCGCACATCTCTCCTCACGCCTCCTGACAGGCTGGGGAGGAGGATGCATCTGGTATCTAGAAAGAAGA
GCCACGCGGGAGTCACCTCGTAGATTCCTGCATCTTCTCAGGAACATCAATCAGCAGTGGGTCACATTTCAACACGTTAA
CTTCCTCCAGCTCATGTACATCACACAACTAAACAGAAGCCTCAAGCAGCAAATAAAACCGAAGCCAGAACCAGCAGAAT
CTCCCTTCCTTGAAAAAACTTCTTTGGATGAGGCCAAAGCTGAAATATGCAAGATGAGACCTCTTGTACCCCCCAGCCTG
TCTCTGCCCAGAAAGCCAAATGAAAAAGCACTGATAGAACTAGAACCCACCTCAGTAATTGAGGGCTCCATAGTTCTGGG
GAAAGAGATGAAAGAAGAGAAGCAGTGGAAAGAGATGTAGCTCCGTGCAGATGATTTGCCGGGAATTCTGGCCCGGCTGT
CCAAAATCAAACTCACAGCCCTGGTCGTCAGCACCACCTCGGCCGGCTTCGTCCTGGCTCCAGCGCCTTTTGACTGGTCC
TGTTCCTGCTTCCTGCTTGCTTTTGTTGGAACAGGCCTGGCTTCCTGCGCTGCCAACTTCATCAATCAGTTTTTTGAGGT
TCCGTTTGATTCAAACATGAACAGGACAAAGAACAGACCTCTGGTTCGTGGACAGATCAGCCCGCTGCTCTCCTTGTCCT
TCGCCACGTGCTGTGAGGTTCCCGGAGTTGCCCTGCTGACCTGGGACGTGAACCCGCTCACGGGGCGCCCTGGGCCTCTT
CAACATTTTCCTGTACACCTTCTGCTACACCCCACTCAAGAGGGTCAGCATCGCCAACACATGGGTGGGGGCGGTCGTGG
GGGCTATTCCCCCATCATGGTCTGGACCGCCGCTACGGGCAGTCTGGATGCTGGGAACTGC

Alignment

ORF - retro_btau_1425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 70.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASPHT-LSSRLLTGWGGGCIWYLERRVTRESPRRFLHLLRNVNQQWVTFQHFNFLRHMYVTQLNRSLK
          MAASPH..LSSRLLTGWGGGCIWYLERR.TRESPRRFLHLLRN.NQQWVTFQH.NFL..MY.TQLNRSLK
Retrocopy MAASPHI<LSSRLLTGWGGGCIWYLERRATRESPRRFLHLLRNINQQWVTFQHVNFLQLMYITQLNRSLK

Parental  QQIKPKPEPAESPFLEKTSLDEAKAEICEMRPLVPPSLSLSRKPSEKALIEPEPTSVIEGSIDLGKETKE
          QQIKPKPEPAESPFLEKTSLDEAKAEIC.MRPLVPPSLSL.RKP.EKALIE.EPTSVIEGSI.LGKE.KE
Retrocopy QQIKPKPEPAESPFLEKTSLDEAKAEICKMRPLVPPSLSLPRKPNEKALIELEPTSVIEGSIVLGKEMKE

Parental  EKQWKEMKLRVDDLPGILARLSKIKLTALVVSTTSAGFALAPAPFDW--SCFLLTFVGTGLASCAANSIN
          EKQWKEM.LR.DDLPGILARLSKIKLTALVVSTTSAGF.LAPAPFDW..SCFLL.FVGTGLASCAAN.IN
Retrocopy EKQWKEM*LRADDLPGILARLSKIKLTALVVSTTSAGFVLAPAPFDWSCSCFLLAFVGTGLASCAANFIN

Parental  QFFEVPFDSNMNRTKNRPLVRGQISPLLAVSFATCCAVPGVALLTWGVNPLT-GALGLFNIFLYTCCYTP
          QFFEVPFDSNMNRTKNRPLVRGQISPLL..SFATCC.VPGVALLTW.VNPLT.GALGLFNIFLYT.CYTP
Retrocopy QFFEVPFDSNMNRTKNRPLVRGQISPLLSLSFATCCEVPGVALLTWDVNPLT>GALGLFNIFLYTFCYTP

Parental  LKRVSIANTWVGAVVGAIP-PVMGWTAATGSLDAGAC
          LKRVSIANTWVGAVVGAIP.P.M.WTAATGSLDAG.C
Retrocopy LKRVSIANTWVGAVVGAIP<PIMVWTAATGSLDAGNC

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	2.96 RPM
ERP005899_muscle	0.05 RPM	21.38 RPM
SRP017611_brain	0.00 RPM	12.47 RPM
SRP017611_kidney	0.00 RPM	13.99 RPM
SRP017611_liver	0.00 RPM	5.36 RPM
SRP030211_testis	0.08 RPM	41.66 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1425 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1425 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015294	1 retrocopy	retro_btau_1425 ,
Canis familiaris	ENSCAFG00000017899	1 retrocopy	retro_cfam_1380,
Callithrix jacchus	ENSCJAG00000004522	1 retrocopy	retro_cjac_3938,
Felis catus	ENSFCAG00000010334	1 retrocopy	retro_fcat_814,
Otolemur garnettii	ENSOGAG00000007457	1 retrocopy	retro_ogar_606,