RetrogeneDB ID: retro_btau_1290

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:84711666..84712071(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000009769
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBP1
• Ensembl ID: ENSBTAG00000020028
• Aliases: RBP1, CRBP1
• Description: Retinol-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P02694]

Sequence

>retro_btau_1290
ATGCCGGTCGACTTTACTGGGTACTGGAAGATGCTGGCCAACGAGAATTTTGAGGAGTACCTGCGCGTGCTGGATGTCAA
TGTGGCCTTGCGCAAAATTGCCAACTTGCTGAAGCCAGACAAAGAGATCGTGCAGGAAGGCGACCACATGATCATCCGCA
TGCTGAGCACTTTTAGAAACTACATCGTGGACTTCCAGGTTGGGAAGGAGTTTGAGGAGGATCTAACAGGCATAGACGAC
CGCAAGTGCATGACTACGGTGAGCTGGGATGGGGACAAGCTCGAGTGTGTGCAGAAGGGCGAGAAGGAGGGACATGGCTG
GACCCAGTGGATTGAGGGTGAGGAGCTGCACCTGGAGATGAGAATGGAGGGTGTGGTCTGCAAGCAAGTATTCAAAAAGG
TGAAC

Alignment

ORF - retro_btau_1290 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPVDFTGYWKMLANENFEEYLRALDVNVALRKIANLLKPDKEIVQEGDHMIIRTLSTFRNYIMDFQVGKE
          MPVDFTGYWKMLANENFEEYLR.LDVNVALRKIANLLKPDKEIVQEGDHMIIR.LSTFRNYI.DFQVGKE
Retrocopy MPVDFTGYWKMLANENFEEYLRVLDVNVALRKIANLLKPDKEIVQEGDHMIIRMLSTFRNYIVDFQVGKE

Parental  FEEDLTGIDDRKCMTTVSWDGDKLECVQKGEKEGRGWTQWIEGDELHLEMRVEGVVCKQVFKKVN
          FEEDLTGIDDRKCMTTVSWDGDKLECVQKGEKEG.GWTQWIEG.ELHLEMR.EGVVCKQVFKKVN
Retrocopy FEEDLTGIDDRKCMTTVSWDGDKLECVQKGEKEGHGWTQWIEGEELHLEMRMEGVVCKQVFKKVN

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	14.92 RPM
ERP005899_muscle	0.00 RPM	21.01 RPM
SRP017611_brain	0.00 RPM	3.56 RPM
SRP017611_kidney	0.18 RPM	15.94 RPM
SRP017611_liver	0.00 RPM	8.31 RPM
SRP030211_testis	0.02 RPM	10.68 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1290 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467, retro_btau_295,
Bos taurus	ENSBTAG00000020028	1 retrocopy	retro_btau_1290 ,
Bos taurus	ENSBTAG00000047330	3 retrocopies	retro_btau_1312, retro_btau_1828, retro_btau_886,
Erinaceus europaeus	ENSEEUG00000005367	1 retrocopy	retro_eeur_42,
Macropus eugenii	ENSMEUG00000003195	2 retrocopies	retro_meug_1379, retro_meug_511,
Ictidomys tridecemlineatus	ENSSTOG00000005673	1 retrocopy	retro_itri_749,