RetrogeneDB ID: retro_btau_1457

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:62543216..62544158(+)
• Located in intron of: ENSBTAG00000020367

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF126
• Ensembl ID: ENSBTAG00000014349
• Aliases: None
• Description: RING finger protein 126 [Source:UniProtKB/Swiss-Prot;Acc:Q0II22]

Sequence

>retro_btau_1457
ATGGCCGAAGCGTCGCCGCAGCCCGGACGGTACTTCTGCCACTGCTGCTCAGTCGAGATCGTGCCGCGCCTGCCGGATTA
CATCTGCCCAAGATGCGGGTCTGGGTTTATCGAGGAGCTTCCAGAAGAGAACAGGAGTGCAGAGAATGGTTCAGCCCCCT
CCACAGCCTCTGCGGACCAGAGCCGGCAGCAACCGTTCGAGAATGTGGACCAGCCCCTGTTCACGCTGCCGCAGGGCTAT
GGGCACTTTGCTTTCGGCATCTTTGACGACAGCTTTGAGATCCCCACGTTCCCCGCTGGGGCACAGGCTGATGATAGCAG
GGACCCCGAGAGCCGGCGGGAGCGAGAGCAGGACTCCTGGCACCCGTACGGCCCCCGGCAGCCCTGCGCCCGCCTCACCG
CGCGGCGGGCCACCGGCCGGCACGAAGGCGACCCCACGCTGGAAGGGATCATCCAGCAGCTGGTCAACGGCATCATCACC
CCGGCCACCATCCCCAACCTGGGCCTGGGTCCCTGGGACGTCCTGCATTCAAACCCGATGGACTACACCTGGGGGGCCAA
CAGCCTGGACGCCATCATCACGCAGCTCCTTAATCAGTTTGAAAACTCGGGTCCCCCACCCGCAGACAAAGAGAAAATCC
AGGCCCTCCCCACCGTGCCCGTGACTGAGGAGCACGTTGGCTCGGGGCTGGAGTGCCCCGTGTGCAAGGATGACTATGGG
CTGGGTGAGCATGTGCGGCAGCTGCCCTGCAACCACTTCTTCCACAATGGCTGCATCGTGCCCTGGCTGGAGCAGCACGA
CAGCTGCCCCGTCTGCCGAAAAAGCCTCACAGGACAGAACACGGCCACTGACCCCCCGGGCCTGGCTGTGGTGAGCTTCT
CCTCCTCCTCCTCCTCCTCGTCCTCCAGCTCACCTGGCAATGAGAACCCGGCCAGCAGCTCC

Alignment

ORF - retro_btau_1457 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEASPQPGRYFCHCCSVEIVPRLPDYICPRCESGFIEELPEETRSAENGSAPSTASADQSRQQPFENVD
          MAEASPQPGRYFCHCCSVEIVPRLPDYICPRC.SGFIEELPEE.RSAENGSAPSTASADQSRQQPFENVD
Retrocopy MAEASPQPGRYFCHCCSVEIVPRLPDYICPRCGSGFIEELPEENRSAENGSAPSTASADQSRQQPFENVD

Parental  QPLFTLPQGYGHFAFGIFDDSFEIPTFPPGAQADDSRDPESRREREQHSRHRYGARQPRARLTARRATGR
          QPLFTLPQGYGHFAFGIFDDSFEIPTFP.GAQADDSRDPESRREREQ.S.H.YG.RQP.ARLTARRATGR
Retrocopy QPLFTLPQGYGHFAFGIFDDSFEIPTFPAGAQADDSRDPESRREREQDSWHPYGPRQPCARLTARRATGR

Parental  HEGVPTLEGIIQQLVNGIITPATIPNLGLGPWGVLHSNPMDYAWGANGLDAIITQLLNQFENTGPPPADK
          HEG.PTLEGIIQQLVNGIITPATIPNLGLGPW.VLHSNPMDY.WGAN.LDAIITQLLNQFEN.GPPPADK
Retrocopy HEGDPTLEGIIQQLVNGIITPATIPNLGLGPWDVLHSNPMDYTWGANSLDAIITQLLNQFENSGPPPADK

Parental  EKIQALPTVPVTEEHVGSGLECPVCKDDYGLGEHVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSLTGQN
          EKIQALPTVPVTEEHVGSGLECPVCKDDYGLGEHVRQLPCNH.FH.GCIVPWLEQHDSCPVCRKSLTGQN
Retrocopy EKIQALPTVPVTEEHVGSGLECPVCKDDYGLGEHVRQLPCNHFFHNGCIVPWLEQHDSCPVCRKSLTGQN

Parental  TATDPPGLAGVSFSSSSSSSSSS-PGNENPASSS
          TATDPPGLA.VS..........S.PGNENPASSS
Retrocopy TATDPPGLAVVSXXXXXXXXXXSSPGNENPASSS

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	5.55 RPM
ERP005899_muscle	0.05 RPM	17.79 RPM
SRP017611_brain	0.09 RPM	26.31 RPM
SRP017611_kidney	0.18 RPM	24.48 RPM
SRP017611_liver	0.08 RPM	30.43 RPM
SRP030211_testis	1.00 RPM	146.28 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1457 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1457 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014349	1 retrocopy	retro_btau_1457 ,
Homo sapiens	ENSG00000070423	1 retrocopy	retro_hsap_1770,
Nomascus leucogenys	ENSNLEG00000000828	1 retrocopy	retro_nleu_2331,