RetrogeneDB ID: retro_btau_670

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:15981281..15981626(-)
• Located in intron of: ENSBTAG00000014111

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GSTA4
• Ensembl ID: ENSBTAG00000004288
• Aliases: None
• Description: Glutathione S-transferase A4 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9G0]

Sequence

>retro_btau_670
GTGTACCCTTACCTCAAACCAGATGATCAGCAAAAGAAAGTGGTTAACATAGCCCAGAAGCTATACTTAGATACTTTCCT
GGGTTTGAAAAGGCTTTACAGAGTCATGGACAAAGGTTTCTTGTTGGCAATCAGCTGAGCCTTGCAGACATAATTCTACT
CCAGATCATTTTGGCTCTAGAAGAAAAAACATCTTAATATTCTGTCTGCCTTCCCTCACCTCCAGGAGTACATGGTGAAA
ATAAGCAAAATCCCTGCAATTAATAAATTCCTTGAACCTGGCAGTGAGAAGCAGCCTCTGCCAGATGACATGTATGTGAA
AACCATGTACAGCATCTTCATGCCA

Alignment

ORF - retro_btau_670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 51.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MHPFLKPDDQQKEVANMAQK-AIIRYFPVFEKVLRGHGQRFLVGNQLSLADIILLQTILALEEKIP-NIL
          ..P.LKPDDQQK.V.N.AQK.AI.RYFP.FEK.L..HGQRFLVGNQLSLADIILLQ.ILALEEK...NIL
Retrocopy VYPYLKPDDQQKKVVNIAQK<AILRYFPGFEKALQSHGQRFLVGNQLSLADIILLQIILALEEKTS>NIL

Parental  SAFPHLQEYTVKISNIPTIKKFLEPGSKKKPPPDDIYVRTVYNIFMP
          SAFPHLQEY.VKIS.IP.I.KFLEPGS.K.P.PDD.YV.T.Y.IFMP
Retrocopy SAFPHLQEYMVKISKIPAINKFLEPGSEKQPLPDDMYVKTMYSIFMP

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	249.81 RPM
ERP005899_muscle	0.00 RPM	14.20 RPM
SRP017611_brain	0.00 RPM	82.09 RPM
SRP017611_kidney	0.06 RPM	46.17 RPM
SRP017611_liver	0.00 RPM	22.12 RPM
SRP030211_testis	0.03 RPM	16.68 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_670 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_670 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
Ailuropoda melanoleuca	ENSAMEG00000005658	1 retrocopy	retro_amel_787,
Bos taurus	ENSBTAG00000004288	1 retrocopy	retro_btau_670 ,
Canis familiaris	ENSCAFG00000024066	1 retrocopy	retro_cfam_1440,
Felis catus	ENSFCAG00000005237	1 retrocopy	retro_fcat_1199,
Monodelphis domestica	ENSMODG00000018810	1 retrocopy	retro_mdom_954,
Mustela putorius furo	ENSMPUG00000008911	1 retrocopy	retro_mputfur_1383,
Sorex araneus	ENSSARG00000009989	1 retrocopy	retro_sara_769,