RetrogeneDB ID: retro_btau_672

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:28834718..28835374(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000021011
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.100842
• Ensembl ID: ENSBTAG00000003401
• Aliases: None
• Description: Actin-related protein 3 [Source:UniProtKB/Swiss-Prot;Acc:P61157]

Sequence

>retro_btau_672
AGGAGGGTGATGAAAGGTGTTGACGACCTAGACTTCTTCATTGGTGATGAAGCAATAGAAAAACCTACATATGCAACGGA
GTGGCCAATCCGCCATGGTATAGTTGAATACTGGGACTTGATGGAAAGGTTTATGGAGCAAGTGATCTTTAAATATTTAA
GGGTGGAACCTGAAGATCATTATTTTCTTTTGACTGAACCTCCACTGAATACTCCAGAAAACAGGGAATACACTGCTGAA
ATAATGTTTGAGTCCTTCAATGTTCCTGGCTTGTACATTGCTGTACAGGCCGTTCTTGCCTTAGCTGCATCTTGGACCTC
CAGACAAGTAGGAGATCGGACATTGACTGGTACGTAATAAGCGGTGGAGATGGAGTCACTCATGTTATCCCTGTGGCTGA
AGGGTATGTGATTGGCAGCTGTATTAAGCACATTCCAATCACAGGATGAGATATAACATATTTTATTCAGCAATTGTTGA
GAAACTGAGAAGTAGGAATTCCTCCAGAGCAATCCTTGGAAACTGCTAAGGCAGTGAAGGAGCACTATAGTTATGTCTGC
CCAGACTTAGTAAAAGAATTTAACAAGTATGATACACATGGATCAAAGTGGATTAAACAGTATACTGAAATCAATGCTAT
CTCAAAGAAAGTTTTC

Alignment

ORF - retro_btau_672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.18 %
• Parental protein coverage: 57.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRVMKGVDDLDFFIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLN
          RRVMKGVDDLDFFIGDEAIEKPTYAT.WPIRHGIVE.WDLMERFMEQVIFKYLR.EPEDHYFLLTEPPLN
Retrocopy RRVMKGVDDLDFFIGDEAIEKPTYATEWPIRHGIVEYWDLMERFMEQVIFKYLRVEPEDHYFLLTEPPLN

Parental  TPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGT-VIDSGDGVTHVIPVAEGYVIG
          TPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVG.RTLTGT.VI..GDGVTHVIPVAEGYVIG
Retrocopy TPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGDRTLTGT<VISGGDGVTHVIPVAEGYVIG

Parental  SCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYT
          SCIKHIPI.G.DITYFIQQLLR..EVGIPPEQSLETAKAVKE.YSYVCPDLVKEFNKYDT.GSKWIKQYT
Retrocopy SCIKHIPITG*DITYFIQQLLRN*EVGIPPEQSLETAKAVKEHYSYVCPDLVKEFNKYDTHGSKWIKQYT

Parental  GINAISKKEF
          .INAISKK.F
Retrocopy EINAISKKVF

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	0.07 RPM	27.97 RPM
ERP005899_muscle	7.18 RPM	139.47 RPM
SRP017611_brain	2.38 RPM	62.63 RPM
SRP017611_kidney	2.85 RPM	76.70 RPM
SRP017611_liver	0.91 RPM	23.86 RPM
SRP030211_testis	4.06 RPM	87.76 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_672 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_672 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003401	1 retrocopy	retro_btau_672 ,
Callithrix jacchus	ENSCJAG00000014091	4 retrocopies	retro_cjac_3602, retro_cjac_3813, retro_cjac_385, retro_cjac_4005,
Homo sapiens	ENSG00000115091	2 retrocopies	retro_hsap_1391, retro_hsap_4694,
Gorilla gorilla	ENSGGOG00000011346	1 retrocopy	retro_ggor_2921,
Mustela putorius furo	ENSMPUG00000010717	1 retrocopy	retro_mputfur_1275,
Mus musculus	ENSMUSG00000026341	1 retrocopy	retro_mmus_3653,
Nomascus leucogenys	ENSNLEG00000011619	2 retrocopies	retro_nleu_1077, retro_nleu_2364,
Pongo abelii	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468,