RetrogeneDB ID: retro_btau_83

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:35101142..35101808(-)
• Located in intron of: ENSBTAG00000001838

Retrocopy information

• Ensembl ID: ENSBTAG00000046690
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB27A
• Ensembl ID: ENSBTAG00000012408
• Aliases: None
• Description: ras-related protein Rab-27A [Source:RefSeq peptide;Acc:NP_001094740]

Sequence

>retro_btau_83
ATGTCTGATGGAGACTATGATTACCTCATCAAGTTTTTAGCTCTGGGAGACTCGGGAGTAGGGAAGACCAGTGTGCTTTA
TCAGTACACAGATGGTAAATTTAACTCCAAATTCATCACAACAGTCGGCATTGATTTCAGGGAAAACAGAGTGGTGTACA
GAGCCAATGGGCCAGATGGAGCTGTTGGCAGAGGTCAGAGAATCCACCTGCAGTTATGGGACACAGCTGGACAAGAGAGG
TTTCGTAGCTTGACAACTGCCTTCTTCAGAGATGCTATGGGGTTTCTTCTGCTTTTTGATCTGACAAATGAGCAGAGTTT
TCTCAATGTCAGAAACTGGATAAGTCAGCTACAAATGCATGCATATTGTGAAAACCCAGATATAGTGTTATGTGGGAATA
AGAGTGATCTGGAAGACCAAAGAGTAGTAAAAGAGGAAGAAGTCAGAGGACTTGCAGAGAAATACGGAGTCCCCTACTTT
GAAACTAGTGCTGCCAATGGGACAAACATAAACCAGGCTATTGAGATGCTCCTGGACCTGATAATGAAGCGAATGGAACG
GTGTATGGACAAGTCCTGGATTCTCGAAGGCGTGGTGCATTCCAACGGTCACACCTCTGCAGATCAGCTGAATGAAGAAA
AGGAGAAGGGGTCATGTGGCTGTTGA

Alignment

ORF - retro_btau_83 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFDGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKFITTVGIDFREKRVVYRANGPDGAVGRGQRIHL
          M.DGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKFITTVGIDFRE.RVVYRANGPDGAVGRGQRIHL
Retrocopy MSDGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKFITTVGIDFRENRVVYRANGPDGAVGRGQRIHL

Parental  QLWDTAGQERFRSLTTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYCENPDIVLCGNKSDLEDQ
          QLWDTAGQERFRSLTTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYCENPDIVLCGNKSDLEDQ
Retrocopy QLWDTAGQERFRSLTTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYCENPDIVLCGNKSDLEDQ

Parental  RVVKEEEARGLAEKYGVPYFETSAANGTNINQAIETLLDLIMKRMERCVDKSWIPEGVVRSNGHTSADQL
          RVVKEEE.RGLAEKYGVPYFETSAANGTNINQAIE.LLDLIMKRMERC.DKSWI.EGVV.SNGHTSADQL
Retrocopy RVVKEEEVRGLAEKYGVPYFETSAANGTNINQAIEMLLDLIMKRMERCMDKSWILEGVVHSNGHTSADQL

Parental  NEVKEKGSCGC
          NE.KEKGSCGC
Retrocopy NEEKEKGSCGC

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	0.43 RPM
ERP005899_muscle	0.16 RPM	9.03 RPM
SRP017611_brain	0.05 RPM	1.87 RPM
SRP017611_kidney	0.24 RPM	7.71 RPM
SRP017611_liver	0.00 RPM	0.83 RPM
SRP030211_testis	1.38 RPM	2.20 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_83 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_83 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_83 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012408	1 retrocopy	retro_btau_83 ,
Otolemur garnettii	ENSOGAG00000010405	1 retrocopy	retro_ogar_2033,