RetrogeneDB ID: retro_btau_1488

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:28373361..28373874(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.70677
• Ensembl ID: ENSBTAG00000014156
• Aliases: None
• Description: protein AMN1 homolog [Source:RefSeq peptide;Acc:NP_001069326]

Sequence

>retro_btau_1488
ATGCCCAGCCCTCAGCGGGTCAGTCAGCTCCCGGATCTATGCCTTTGGTGCTTCATGAAGGATATTTCTAGATATATCAC
AGACATTAAGCCTTTGCCACCCAACATAAAAGATAGACTCATCAAAATTATGAGCGTGCAGGGGCAGATAACAGATTCAA
ACATAAGTGAGATTTTACATCCTTTAGTCCAAACTCTAGATCTACGAAGCTGTGATATTTCAGATACTGCTCTCCTGCAC
CTGTGTAACTGTAGAAAACTGAAGAAATTAAATTGAAATTCCTCAAAAGAAAACAGAATTTCCATAACTTCAAAAGGAAT
AAAAGCTGTGGCTTCATCTTGTTCTTACCTGCATGAAGCTTCTTTGAAAAGATGCTGCAATCTCACTGATGAAGGAGTCC
TTGCTCTTGCACTCAATTGCCGGCTGTTAAAGATCATTGACTTAGGAGGCTGCTTAGGTATTACTGATGTGTTCTTGCAG
GCATTAGGAGAAAACTGTGCATTTTTGCAGTGT

Alignment

ORF - retro_btau_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 66.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSPQRVSQLLDLCLWCFMKNISRYITDIKPLPPNIKDRLIKIMSVQGQITDSNISEILHPEVQTLDLRS
          MPSPQRVSQL.DLCLWCFMK.ISRYITDIKPLPPNIKDRLIKIMSVQGQITDSNISEILHP.VQTLDLRS
Retrocopy MPSPQRVSQLPDLCLWCFMKDISRYITDIKPLPPNIKDRLIKIMSVQGQITDSNISEILHPLVQTLDLRS

Parental  CDISDTALLHLCNCRKLKKLNLNSSKENRISITSKGIKAVASSCSYLHEASLKRCCNLTDEGVLALALNC
          CDISDTALLHLCNCRKLKKLN.NSSKENRISITSKGIKAVASSCSYLHEASLKRCCNLTDEGVLALALNC
Retrocopy CDISDTALLHLCNCRKLKKLN*NSSKENRISITSKGIKAVASSCSYLHEASLKRCCNLTDEGVLALALNC

Parental  RLLKIIDLGGCLGITDVSLQALGENCAFLQC
          RLLKIIDLGGCLGITDV.LQALGENCAFLQC
Retrocopy RLLKIIDLGGCLGITDVFLQALGENCAFLQC

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	8.87 RPM
ERP005899_muscle	0.00 RPM	3.06 RPM
SRP017611_brain	0.00 RPM	18.36 RPM
SRP017611_kidney	0.00 RPM	8.42 RPM
SRP017611_liver	0.00 RPM	0.83 RPM
SRP030211_testis	0.15 RPM	141.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1488 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014156	1 retrocopy	retro_btau_1488 ,
Canis familiaris	ENSCAFG00000010668	1 retrocopy	retro_cfam_1650,
Choloepus hoffmanni	ENSCHOG00000008485	2 retrocopies	retro_chof_1418, retro_chof_1459,