RetrogeneDB ID: retro_btau_314

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:131498899..131499772(-)
• Located in intron of: ENSBTAG00000006909

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASCC1
• Ensembl ID: ENSBTAG00000000392
• Aliases: None
• Description: activating signal cointegrator 1 complex subunit 1 [Source:RefSeq peptide;Acc:NP_001069509]

Sequence

>retro_btau_314
ATGGAAGTTCTGCGTCCACAGCTTATAAAAATTGGTGGACGGGTTTATAGGAAGAATCCCATCCAAGAACAGACTTATCA
ACATGAAAAAGAAGATGATGACTATTACCAAGGTCTCGTGGAGTGTTCAGAAGAGCCCTGTGAAACCTACGAGGTGGTGC
AGACCCCACAAGGTTTCCGATGTACCGTGAAGGCCCCCAGCCTACTCTACAAGCATATTGTTGGAAAGAGAGGGGACACT
AGAAAGAAACTAGAAGTGGAGACCAAAACTTCTATTAGCATTCCTAAGCCTGGACAAGAAGGAGAAATTGTAATCACTGG
TCAGCATCGAAGTGGTGTAATTTCAGCCTGAACTCGGATTGATGTTCTTCTGGTCACTTTTAGAAGAAAGCAGCCCTTCA
CTCACTTCCTTGCCTTTTTCCTCAATGAAGCTGAAGTTCAGGAACGATTTCTGAAATTCCAGGAGGAAGTACTGGAGAAG
TGCTCCATGGATCATGGGGTTGATAGCAGCATTTTCCAGAATCCTAAAAAGCTTCACCTAACTATTGGGATGTTGGTGCT
TTTGAGTGAGCAAGAGATCCAGCAGACATGTGAGATGCTACAGCAGTGTAAAGAGGAATTCATTGATGACATTTCAGGGG
GCAAACCCCTGGAAGTAGAGATGTCAGGGATAGAATACATGAATGATGATCCTGGCATGGTGGATGTTCTTTATGCCAAA
GTCCATATGAAAGATGGCTCCAACAGGCTGCAGGAATTGGTTGATCGAGTGCTGGAACGTTTTCAGGCATCTGGACTAAT
AGTGAAAGAGTGGAATAGTGTGAAACTCCATGCTACAGTCATGAATACTCTGTTCAGGAAAGACCCCAATGCT

Alignment

ORF - retro_btau_314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.28 %
• Parental protein coverage: 81.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVLRPQLIKIGGRVYRKNPIQEQTYQHEEEDDDYYQGLVECAEEPCETYEVVQTPQGFRCTVKAPSLLY
          MEVLRPQLIKIGGRVYRKNPIQEQTYQHE.EDDDYYQGLVEC.EEPCETYEVVQTPQGFRCTVKAPSLLY
Retrocopy MEVLRPQLIKIGGRVYRKNPIQEQTYQHEKEDDDYYQGLVECSEEPCETYEVVQTPQGFRCTVKAPSLLY

Parental  KHIVGKRGDTRKKLEVETKTSISIPKPGQEGEIVITGQHRSGVVSARTRIDVLLLTFRRKQPFTHFLAFF
          KHIVGKRGDTRKKLEVETKTSISIPKPGQEGEIVITGQHRSGV.SA.TRIDVLL.TFRRKQPFTHFLAFF
Retrocopy KHIVGKRGDTRKKLEVETKTSISIPKPGQEGEIVITGQHRSGVISA*TRIDVLLVTFRRKQPFTHFLAFF

Parental  LNEAEVQERFLKFQEEVLEKCSMDHGVDSSIFQNPKKLHLTIGMLVLLSEQEIQQTCEMLQQCKEEFIDD
          LNEAEVQERFLKFQEEVLEKCSMDHGVDSSIFQNPKKLHLTIGMLVLLSEQEIQQTCEMLQQCKEEFIDD
Retrocopy LNEAEVQERFLKFQEEVLEKCSMDHGVDSSIFQNPKKLHLTIGMLVLLSEQEIQQTCEMLQQCKEEFIDD

Parental  ISGGKPLEVEMSGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNSVKLHATV
          ISGGKPLEVEMSGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNSVKLHATV
Retrocopy ISGGKPLEVEMSGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNSVKLHATV

Parental  MNTLFRKDPNA
          MNTLFRKDPNA
Retrocopy MNTLFRKDPNA

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	6.20 RPM
ERP005899_muscle	0.00 RPM	20.75 RPM
SRP017611_brain	0.41 RPM	11.05 RPM
SRP017611_kidney	0.65 RPM	16.77 RPM
SRP017611_liver	0.00 RPM	3.32 RPM
SRP030211_testis	0.22 RPM	15.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_314 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_314 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000392	1 retrocopy	retro_btau_314 ,