RetrogeneDB ID: retro_btau_1605

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:38401079..38401508(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000005972
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.23510
• Ensembl ID: ENSBTAG00000011625
• Aliases: None
• Description: acyl-protein thioesterase 2 [Source:RefSeq peptide;Acc:NP_001073831]

Sequence

>retro_btau_1605
GAGGCTGGCATCAAGAAAGCAACAGAGAATATCAAGGCCTTGATTGAGCATGAGATGAAGAATGGGATCCCTGCCAATCG
GATCGTCCTGGGACGCTTTTCACAGGGTGGAGCTTTGTCCCTCTACACAGCCCTCACCTGCTCACACCCTCTGGCTGGCA
CTGTGGCATTGAGCTGTTGGCTACCTCTGCATCGGGCCTCCCCCCAGGCAGCCAATGGTAGTGCCAAAGACCTGACCATC
CTTCAGTGCCGAGGGGAGCTGGACCCCATGGTTCCTGTACGGTTTGGGGCCCTGACAGCCGAGAAGCTCTGGTCCATTGT
CACACCTGCCAGGGTCCAGTTCAAGAAGTACCCAGGTGTCACGCATAGCCCCTGTCCTCAGGAGATGGCAGCTGTGAAGA
AGTTTCTCGAGAAGCTGCTGCCTCCTGTC

Alignment

ORF - retro_btau_1605 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAGIKKAAENIKALIEHEMKNGIPANRIVLGGFSQGGALSLYTALTCPHPLAGIVALSCWLPLHRAFPQA
          EAGIKKA.ENIKALIEHEMKNGIPANRIVLG.FSQGGALSLYTALTC.HPLAG.VALSCWLPLHRA.PQA
Retrocopy EAGIKKATENIKALIEHEMKNGIPANRIVLGRFSQGGALSLYTALTCSHPLAGTVALSCWLPLHRASPQA

Parental  ANGSAKDLTILQCHGELDPMVPVRFGALTAEKLRSVVTPARVQFKTYPGVMHSSCPQEMAAVKEFLEKLL
          ANGSAKDLTILQC.GELDPMVPVRFGALTAEKL.S.VTPARVQFK.YPGV.HS.CPQEMAAVK.FLEKLL
Retrocopy ANGSAKDLTILQCRGELDPMVPVRFGALTAEKLWSIVTPARVQFKKYPGVTHSPCPQEMAAVKKFLEKLL

Parental  PPV
          PPV
Retrocopy PPV

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	2.02 RPM
ERP005899_muscle	0.21 RPM	16.58 RPM
SRP017611_brain	0.32 RPM	9.82 RPM
SRP017611_kidney	0.47 RPM	14.82 RPM
SRP017611_liver	0.38 RPM	13.36 RPM
SRP030211_testis	0.51 RPM	10.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1605 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1605 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1605 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011625	1 retrocopy	retro_btau_1605 ,
Callithrix jacchus	ENSCJAG00000020914	1 retrocopy	retro_cjac_2585,
Dasypus novemcinctus	ENSDNOG00000011285	2 retrocopies	retro_dnov_1186, retro_dnov_134,
Homo sapiens	ENSG00000011009	3 retrocopies	retro_hsap_2023, retro_hsap_3577, retro_hsap_4180,
Gorilla gorilla	ENSGGOG00000004330	3 retrocopies	retro_ggor_2114, retro_ggor_2413, retro_ggor_2626,
Macropus eugenii	ENSMEUG00000004768	2 retrocopies	retro_meug_1134, retro_meug_1526,
Microcebus murinus	ENSMICG00000005841	1 retrocopy	retro_mmur_1166,
Nomascus leucogenys	ENSNLEG00000008646	1 retrocopy	retro_nleu_2958,
Otolemur garnettii	ENSOGAG00000032260	1 retrocopy	retro_ogar_2866,
Pongo abelii	ENSPPYG00000001733	1 retrocopy	retro_pabe_142,
Tursiops truncatus	ENSTTRG00000016127	1 retrocopy	retro_ttru_1522,