RetrogeneDB ID: retro_btau_1564

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:22831361..22831913(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000025445
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSBTAG00000008967
• Aliases: None
• Description: Ras-related protein Rap-1b [Source:UniProtKB/Swiss-Prot;Acc:P61223]

Sequence

>retro_btau_1564
ATGCGTGAGTATAAGCTAGTCGTTCTTGGCTCGGGAGGCGTTGGAAAATCTGCTCTGACTGTACAGTTTGTTCAAGGAAT
TTTTGTTGAAAAATATGATCCTACGATAGAAGATTCTTATAGAAAGCAAGTTGAAGTAGATGCACAGCAGTGTATGCTTG
AAATCTTGGATACTGCAGGAACGGAACAATTCACAGCAATGAGGGATTTGTACATGAAAAATGGACAAGGCTTTGCGTTA
GTTTATTCCATCACAGCACAGTCCACATTTAATGATTTACAAGATCTGAGAGAACAGATTCTTCGAGTTAAAGACACAGA
TGATGTTCCAATGATTCTGGTTGGTAGTAAGTGTGACTTGGAAGATGAAAGAGTTGTAGGAAAGGAACAAGGTCAAAATC
TAGCAAGACAGTGGAACAACTGTGCATTCTTAGAATCCTCTGCAAAATCAAAAATAAATGTTAATGAGATCTTTTATGAC
CTAGCGCGACAAATTAACAGAAAAACTCCAGTGCCTGGGAAAGCCCACAAAAAGTCGTCATGTCAGCTGCTT

Alignment

ORF - retro_btau_1564 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
          MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
Retrocopy MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL

Parental  YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNN
          YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVG.KCDLEDERVVGKEQGQNLARQWNN
Retrocopy YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGSKCDLEDERVVGKEQGQNLARQWNN

Parental  CAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          CAFLESSAKSKINVNEIFYDL.RQINRKTPVPGKA.KKSSCQLL
Retrocopy CAFLESSAKSKINVNEIFYDLARQINRKTPVPGKAHKKSSCQLL

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	45.28 RPM
ERP005899_muscle	0.11 RPM	58.75 RPM
SRP017611_brain	0.09 RPM	29.69 RPM
SRP017611_kidney	0.18 RPM	61.64 RPM
SRP017611_liver	0.08 RPM	15.33 RPM
SRP030211_testis	0.04 RPM	42.45 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1564 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1564 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Bos taurus	ENSBTAG00000008967	3 retrocopies	retro_btau_1564 , retro_btau_297, retro_btau_684,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,