RetrogeneDB ID: retro_btau_560

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:43782415..43783041(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000009539
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACAT2
• Ensembl ID: ENSBTAG00000002827
• Aliases: None
• Description: acetyl-CoA acetyltransferase, cytosolic [Source:RefSeq peptide;Acc:NP_001069017]

Sequence

>retro_btau_560
ATGAGTGCAGACTTGGACCCAGTGGTCCTTGTCTCGGCAGCGCGCACCATCATAGGCTCTTTCAATGGTGCCTTACCCAC
TGTTCCTGTCCATGACCTGGGCTCAACTGTTAGAGAGGTCCTGAAAAGGGTGCTGTGGCTCCCAAAGAGGTCTCAGAGGT
CATATTTAGACACTTTTTGGCAGTAGGCTGTGGGCAGAACCCTGTTGGACAGGCCAGTGTGGGTGCGGGAATCCCCTACT
TTGTTCCAGCGTGGAGCTGCCAAATGATCTGCAGGTCAGGTCTGAAAGCCGTGGGTCTCGCAGCCCAATCGATAAGGATA
GGAGACTCCAGCATTGTTGCAGGAGGCATGGAAAAATATGAGCAAGGCTCCTCATTTGGTTCACTTGAGGATGGGAGTCA
AGACTGGGGAAAAACCACTGACAGACAGTATACTCTGTGACGGGCTCACTGACGTATTCCACGACTATCATATGGGCATT
ACAGCTGAAAATGTGGCCAAACAGTGGCAAGTGGGTAGAGAAGACAGGCCAAGGTTGCCGTGCTGTCCCAGAACAGGACG
GAGAATGCACAGAAGGCCGGCCATTTTGACAAAGAGATTGTTCCAGTTTTTGTATCTTCTAAAAAA

Alignment

ORF - retro_btau_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 53.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSADSDPVVIVSAARTIIGSFNGALSTVPVHDLGSTVIREVLKRA-AVAPEEVSEVIFGHVLAAGCGQNP
          MSAD.DPVV.VSAARTIIGSFNGAL.TVPVHDLGSTV.REVLKR..AVAP.EVSEVIF.H.LA.GCGQNP
Retrocopy MSADLDPVVLVSAARTIIGSFNGALPTVPVHDLGSTV-REVLKRV<AVAPKEVSEVIFRHFLAVGCGQNP

Parental  VRQASVGAGIPYSVPAWSCQMICGSGLKAVCLAAQSIRIGDSSIVVAGGME-NMSKAPHLVHLRTGVKIG
          V.QASVGAGIPY.VPAWSCQMIC.SGLKAV.LAAQSIRIGDSSIV.AGGME.NMSKAPHLVHLR.GVK.G
Retrocopy VGQASVGAGIPYFVPAWSCQMICRSGLKAVGLAAQSIRIGDSSIV-AGGME>NMSKAPHLVHLRMGVKTG

Parental  ETPLADSILCDGLTDAFHNYHMGITAENVAKQWQVSRED-QDKVAVLSQNRTEHAQKAGHFDKEIVPVFV
          E.PL.DSILCDGLTD.FH.YHMGITAENVAKQWQV.RED.Q.KVAVLSQNRTE.AQKAGHFDKEIVPVFV
Retrocopy EKPLTDSILCDGLTDVFHDYHMGITAENVAKQWQVGRED<QAKVAVLSQNRTENAQKAGHFDKEIVPVFV

Parental  SSKK
          SSKK
Retrocopy SSKK

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	83.70 RPM
ERP005899_muscle	0.00 RPM	52.74 RPM
SRP017611_brain	0.00 RPM	23.52 RPM
SRP017611_kidney	0.00 RPM	28.63 RPM
SRP017611_liver	0.00 RPM	57.61 RPM
SRP030211_testis	0.02 RPM	11.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_560 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002827	1 retrocopy	retro_btau_560 ,
Callithrix jacchus	ENSCJAG00000011777	1 retrocopy	retro_cjac_1372,
Dasypus novemcinctus	ENSDNOG00000002502	1 retrocopy	retro_dnov_331,
Macaca mulatta	ENSMMUG00000012843	1 retrocopy	retro_mmul_277,
Monodelphis domestica	ENSMODG00000007156	1 retrocopy	retro_mdom_1493,
Rattus norvegicus	ENSRNOG00000019189	1 retrocopy	retro_rnor_1055,
Xenopus tropicalis	ENSXETG00000021174	1 retrocopy	retro_xtro_45,