RetrogeneDB ID: retro_btau_1248

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:6938877..6939732(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000001608
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STAR
• Ensembl ID: ENSBTAG00000033345
• Aliases: None
• Description: Steroidogenic acute regulatory protein, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q28918]

Sequence

>retro_btau_1248
ATGCTTCTCGCGACGTTTAAGCTGTGTGCCGGAAGCTCCTACAGACACGTGCGCAGCATGAAGGGGCTGCAGCAGCAGGC
TGTGCTGGCCATCGGCCAGGAGCTCAACCGGAGGGCCCTAGGGGGCCCGGCCCCAGCTGCGTGGATTAACCAGGTTCGGC
GTCGCGGCTCTCTCCTAGGTTCTCAGCTGGAAGACCCTCTCTACAGCAACCAAGAGCTGGCCTATATCCAGCAGGGAGAG
GAGGCCATGCAAAGGGCCCTGGGCATCCTCAAAGACCAGGAGGGCTGGAAGAAGGAGAGCCGGCAGGCCAATGGGGACGA
GGTGCTGAGTAAAGTGATCCCTGACGTGGGCAAGGTGTTCCGGTTGGAGGTGGTGGTGCACCAGCCCATGGAGAGGCTTT
ATGAAGAGCTTGTGGAGCGCATGGAGGCCATGGGCGAGTGGAATCCCAATGTCAAGGAGATCAAGGTCCTGCAGAAGATT
GGAAAAGACACGGTCATCACTCATGAGTTGGCTGCAGAGGCGGCAGGAAACCTCGTGGGGCCCCGAGACTTTGTGAGCGT
AGGCTGTACCAAGCGCCGGGGCTCCATGTGTGTGCTGGCTGGCATGGCCACACTCTATGAGGAGATGCCCCAGCAGAAGG
GTGTCATCAGAGCTGAGCACGGCCCCACCTGCATGGTGCTCCGCCCCTTGGCTGGAAGTCCCTCAAGGACCAAACTCACC
TGGCTGCTCAGCATTGACCTCAAGGGATGGCTGCCGAAGACCATCATCAACCAGGTCCTCTCGCAGACCCAGGTGGATTT
TGCCAATCACCTGCGCAAGCGCCTGGAGTCCTGCCCTGCTCTTGAAGCCAGGTGT

Alignment

ORF - retro_btau_1248 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLATFKLCAGSSYRHVRSMKGLQQQAVLAIGQELNRRALGGPAPAAWINQVRRRGSLLGSQLEDPLYSD
          MLLATFKLCAGSSYRHVRSMKGLQQQAVLAIGQELNRRALGGPAPAAWINQVRRRGSLLGSQLEDPLYS.
Retrocopy MLLATFKLCAGSSYRHVRSMKGLQQQAVLAIGQELNRRALGGPAPAAWINQVRRRGSLLGSQLEDPLYSN

Parental  QELAYIQQGEEAMQRALGILKDQEGWKKESRQANGDEVLSKVIPDVGKVFRLEVVVDQPMERLYEELVER
          QELAYIQQGEEAMQRALGILKDQEGWKKESRQANGDEVLSKVIPDVGKVFRLEVVV.QPMERLYEELVER
Retrocopy QELAYIQQGEEAMQRALGILKDQEGWKKESRQANGDEVLSKVIPDVGKVFRLEVVVHQPMERLYEELVER

Parental  MEAMGEWNPNVKEIKVLQKIGKDTVITHELAAEVAGNLVGPRDFVSVRCTKRRGSMCVLAGMATLYEEMP
          MEAMGEWNPNVKEIKVLQKIGKDTVITHELAAE.AGNLVGPRDFVSV.CTKRRGSMCVLAGMATLYEEMP
Retrocopy MEAMGEWNPNVKEIKVLQKIGKDTVITHELAAEAAGNLVGPRDFVSVGCTKRRGSMCVLAGMATLYEEMP

Parental  QQKGVIRAEHGPTCMVLRPLAGSPSRTKLTWLLSIDLKGWLPKTIINQVLSQTQVDFANHLRKRLESCPA
          QQKGVIRAEHGPTCMVLRPLAGSPSRTKLTWLLSIDLKGWLPKTIINQVLSQTQVDFANHLRKRLESCPA
Retrocopy QQKGVIRAEHGPTCMVLRPLAGSPSRTKLTWLLSIDLKGWLPKTIINQVLSQTQVDFANHLRKRLESCPA

Parental  LEARC
          LEARC
Retrocopy LEARC

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	4.11 RPM
ERP005899_muscle	0.00 RPM	0.90 RPM
SRP017611_brain	0.00 RPM	3.93 RPM
SRP017611_kidney	0.00 RPM	2.79 RPM
SRP017611_liver	0.15 RPM	1.21 RPM
SRP030211_testis	0.58 RPM	212.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1248 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1248 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033345	3 retrocopies	retro_btau_1248 , retro_btau_743, retro_btau_744,
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Homo sapiens	ENSG00000147465	1 retrocopy	retro_hsap_1273,
Gorilla gorilla	ENSGGOG00000005787	1 retrocopy	retro_ggor_1000,
Pongo abelii	ENSPPYG00000018520	1 retrocopy	retro_pabe_1057,