RetrogeneDB ID: retro_btau_1111

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:5717209..5718148(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000039406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.58717
• Ensembl ID: ENSBTAG00000002049
• Aliases: None
• Description: hydroxyacyl-coenzyme A dehydrogenase, mitochondrial [Source:RefSeq peptide;Acc:NP_001039799]

Sequence

>retro_btau_1111
ATGGCTTTCGTGACCAGGCAGTTCGTGCGCTCCATGTCCTCCTCCTCCAGCGCCTCGGCCTCGGCGAAAAAAATCCTCGT
CAAGCACGTGACTGTCATCGGCGGTGGGCTGATGGGCGCCGGCATTGCCCAGGTTGCTGCAGCAACTGGCCACACAGTAG
TGTTGGTGGACCAAACAGAGGACATCCTGGAAAAATCTAGAAAGGGAATTGAGGAAAGTCTTCGGAAAGTGGCCAAGAAG
AAGTTTGCAGAAAACCCCAAGGGCACTGATGAGTTTGTGGCGAAGACCCTGAGCAGCATATCGACCAGCACGGATGCAGC
ATCTGTGGTCCACAGCACAGACTTGGTGGTGGCCATCGTAGAGAATCTGCAGATGAAGAACGAGCTGTTCAAGAGGCTGG
ACAAGTTTGCCGCCGAACACACAATCTTTGCCAGCAACACTTCCTCTTTGCAGATCACAAGCCTAGCCAATTCCACCACC
AGACAGGACCGATTCGCCGGGCTCCATTTCTTCAACCCAGTGCCTTTGATGAAGCTTGTGGAGGTCATTAAAACACCAAT
GACCAGCCAGAAGACATTTGAATCTCTGCTAGACTTCAGCAGAGCCCTGGGGAAGCAACCTGTTGCTTGCAAGGACACGC
CTGGGTTTATCGTGAACCGTCTTCTGGTGCCGTACCTCATGGAAGCGGTCAGGCTGTGTGAGCGAGGTGAAGCATCGAAG
GAGGACATCGACACGGCGATGAAGCTGGGCGCCGGCTACCCCATGGGTCCGTTTGAGCTTCTCGATTATGTTGGGCTGGA
TACTACGAAGTTCATCCTAGATGGTTGGCATGAAATGGACTCAAAGAACCCCCTGTTTCAGCCCTGCCCATCCCTGAATA
AGCTGGTAGCAGAGAAAAAGTTTGGCAAGAAATCTGGAGAAGGATTTTACAAATACAAG

Alignment

ORF - retro_btau_1111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFVTRQFVRSMSSSSSAAASAKKILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILEKSRKGI
          MAFVTRQFVRSMSSSSSA.ASAKKILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILEKSRKGI
Retrocopy MAFVTRQFVRSMSSSSSASASAKKILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILEKSRKGI

Parental  EESLRKVAKKKFAENPKGADEFVAKTLSSISTSTDAASVVHSTDLVVEAIVENLQMKNELFKRLDKFAAE
          EESLRKVAKKKFAENPKG.DEFVAKTLSSISTSTDAASVVHSTDLVV.AIVENLQMKNELFKRLDKFAAE
Retrocopy EESLRKVAKKKFAENPKGTDEFVAKTLSSISTSTDAASVVHSTDLVV-AIVENLQMKNELFKRLDKFAAE

Parental  HTIFASNTSSLQITSLANSTTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLLDFSRALGKHPVA
          HTIFASNTSSLQITSLANSTTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLLDFSRALGK.PVA
Retrocopy HTIFASNTSSLQITSLANSTTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLLDFSRALGKQPVA

Parental  CKDTPGFIVNRLLVPYLMEAVRLCERGEASKEDIDMAMKLGAGYPMGPFELLDYVGLDTTKFILDGWHEM
          CKDTPGFIVNRLLVPYLMEAVRLCERGEASKEDID.AMKLGAGYPMGPFELLDYVGLDTTKFILDGWHEM
Retrocopy CKDTPGFIVNRLLVPYLMEAVRLCERGEASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFILDGWHEM

Parental  DSKNPLFQPCPSLNKLVAEKKFGKKSGEGFYKYK
          DSKNPLFQPCPSLNKLVAEKKFGKKSGEGFYKYK
Retrocopy DSKNPLFQPCPSLNKLVAEKKFGKKSGEGFYKYK

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	183.05 RPM
ERP005899_muscle	0.63 RPM	183.23 RPM
SRP017611_brain	0.14 RPM	18.77 RPM
SRP017611_kidney	0.71 RPM	242.36 RPM
SRP017611_liver	0.15 RPM	47.19 RPM
SRP030211_testis	0.10 RPM	23.45 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1111 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002049	2 retrocopies	retro_btau_1111 , retro_btau_1685,
Callithrix jacchus	ENSCJAG00000015938	1 retrocopy	retro_cjac_772,
Echinops telfairi	ENSETEG00000013807	1 retrocopy	retro_etel_1694,
Felis catus	ENSFCAG00000022260	1 retrocopy	retro_fcat_1225,
Homo sapiens	ENSG00000138796	1 retrocopy	retro_hsap_1571,
Gorilla gorilla	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,