RetrogeneDB ID: retro_btau_1729

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:9100506..9101365(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046818
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APEX1
• Ensembl ID: ENSBTAG00000002745
• Aliases: APEX1, APEN, BAP1, REF-1
• Description: DNA-(apurinic or apyrimidinic site) lyase DNA-(apurinic or apyrimidinic site) lyase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P23196]

Sequence

>retro_btau_1729
AGGAGTGAAAAAGAGGCAGCAGGAGAGGACGCAGTTCTGTATGAAGACTCCCAGATCAGAAAACTTCACCCAGTGGCAAA
TCAGCCACACTCAGGCTCTGCTCGTGGAATGTGGATGGGCTTCAAACCTGGATTAAGAAGAAATGTTTAGATTGGGTAAA
GAAGAAGCCCCAGATATCCTGTGCCTCCAAGAGACCAAATGTTCAGAGAACAAACTACCAGTTGAACTTCAAGAGCTGTC
TGGGTTATCCCATCAGTACTGGTCAGCTCCTTCAGACAAGGAGGGGTACAGTGGTGTGGGCCTCCTCTCCCATCAGTGCC
CACTCAAAGTCTCCTATGGCATTGGTGAGGAAGAACATGATCAGGAAGGCCGAGTGATTGTGGCTGAAGATGATGCATTT
GTGCTGGTGACAGCCTATGTGCCTAATGCAGGAGGAGGTCTGGTACACCTGAAGTACCGCCAGCACTGGGATAAAGCCTT
TTGCAAATTCCTGAAGGGTTTGGCATCCTGCAAGCCCCTTGTGCTATGTGGGGACCTCAACGTGGCTCATGAAGAAATTG
CCCTTCGCAACCCAAAGGGAAATAAAAAGAATGCTGGCTTCACTCCACAAGAGCAGCAGGGCTTCGGGAAACTGCTGCAG
GCTGTGCCCCTCAGTGACAGTTCCCAGCACCTCTACCCCAACACAGCCTACGCTTACACCTTTTGGACCTATATGATGAA
CGCACAATCCTAAAACATTGGTTGGTGCCTTGATTATTTTTAGTTATCTCGGTCTCTGTTGCCTGCATTGTGTGACAGCA
AAATCCATTCCAAGGCTCTGGGCAGTGACCACTGTCCCAATACCCTATACCTAGCCCTA

Alignment

ORF - retro_btau_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.89 %
• Parental protein coverage: 90.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KNEKEAVGEGAVLYEDP-PDQKTSPSGKSATLKICSWNVDGLRAWIKKKGLDWV-KEEAPDILCLQETKC
          ..EKEA.GE.AVLYED..PDQKTSPSGKSATL..CSWNVDGL..WIKKK.LDWV.KEEAPDILCLQETKC
Retrocopy RSEKEAAGEDAVLYEDS<PDQKTSPSGKSATLRLCSWNVDGLQTWIKKKCLDWV<KEEAPDILCLQETKC

Parental  SENKLPVELQELSGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGEEEHDQEGRVIVAEYDAFVLVT
          SENKLPVELQELSGLSHQYWSAPSDKEGYSGVGLLS.QCPLKVSYGIGEEEHDQEGRVIVAE.DAFVLVT
Retrocopy SENKLPVELQELSGLSHQYWSAPSDKEGYSGVGLLSHQCPLKVSYGIGEEEHDQEGRVIVAEDDAFVLVT

Parental  AYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQG
          AYVPNAG.GLV.L.YRQ.WD.AF.KFLKGLAS.KPLVLCGDLNVAHEEI.LRNPKGNKKNAGFTPQE.QG
Retrocopy AYVPNAGGGLVHLKYRQHWDKAFCKFLKGLASCKPLVLCGDLNVAHEEIALRNPKGNKKNAGFTPQEQQG

Parental  FGELLQAVPLTDSFRHLYPNTAYAYTFWTYMMNARSKNVGWRLDYFLLSQSLLPALCDSKIRSKALGSDH
          FG.LLQAVPL.DS..HLYPNTAYAYTFWTYMMNA.S.N.GW.LDYF.LS.SLLPALCDSKI.SKALGSDH
Retrocopy FGKLLQAVPLSDSSQHLYPNTAYAYTFWTYMMNAQS*NIGWCLDYF*LSRSLLPALCDSKIHSKALGSDH

Parental  CPITLYLAL
          CP.TLYLAL
Retrocopy CPNTLYLAL

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	34.61 RPM
ERP005899_muscle	0.00 RPM	61.08 RPM
SRP017611_brain	0.00 RPM	34.49 RPM
SRP017611_kidney	0.00 RPM	41.25 RPM
SRP017611_liver	0.00 RPM	29.90 RPM
SRP030211_testis	0.01 RPM	38.44 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1729 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1729 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002745	1 retrocopy	retro_btau_1729 ,
Echinops telfairi	ENSETEG00000004855	1 retrocopy	retro_etel_1392,
Loxodonta africana	ENSLAFG00000021872	1 retrocopy	retro_lafr_948,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027, retro_mmus_433,
Otolemur garnettii	ENSOGAG00000013335	3 retrocopies	retro_ogar_1284, retro_ogar_2145, retro_ogar_3243,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971,
Ictidomys tridecemlineatus	ENSSTOG00000010096	1 retrocopy	retro_itri_1560,
Tupaia belangeri	ENSTBEG00000006405	1 retrocopy	retro_tbel_3409,