RetrogeneDB ID: retro_btau_95

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:68078642..68078846(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000045729
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: C6H4orf52
• Ensembl ID: ENSBTAG00000003897
• Aliases: SMIM20, C6H4orf52
• Description: None

Sequence

>retro_btau_95
ATGTCCCGGAACCTGCGCACTGCTCTCATTTTCGGCGGCTTCATCTCCCTGATCGGCGCCGCCTTCTACCCCATCTACTT
CCGGCCCTTAATGCGGCTGGAGGAGTACAAGAAGGAACAAGCCATAAATCGAGCTGGTATTGTTCAAGAAGACGTGCAGC
CACCAGGGTTGAAAGTGTGGTCGGATCCATTTGGCCGGAAATGA

Alignment

ORF - retro_btau_95 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MSRNLRTALIFGGFISLIGAAFYPIYFRPLMRLEEYKKEQAINRAGIVQEDVQPPGLKVWSDPFGRK
          MSRNLRTALIFGGFISLIGAAFYPIYFRPLMRLEEYKKEQAINRAGIVQEDVQPPGLKVWSDPFGRK
Retrocopy MSRNLRTALIFGGFISLIGAAFYPIYFRPLMRLEEYKKEQAINRAGIVQEDVQPPGLKVWSDPFGRK

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	3.24 RPM
ERP005899_muscle	0.11 RPM	9.03 RPM
SRP017611_brain	0.05 RPM	3.43 RPM
SRP017611_kidney	0.06 RPM	5.10 RPM
SRP017611_liver	0.00 RPM	2.72 RPM
SRP030211_testis	0.35 RPM	3.66 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_95 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_95 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_95 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003897	1 retrocopy	retro_btau_95 ,
Dasypus novemcinctus	ENSDNOG00000004966	2 retrocopies	retro_dnov_1474, retro_dnov_1529,
Macropus eugenii	ENSMEUG00000002680	1 retrocopy	retro_meug_147,
Microcebus murinus	ENSMICG00000017222	1 retrocopy	retro_mmur_868,
Macaca mulatta	ENSMMUG00000006680	1 retrocopy	retro_mmul_179,
Nomascus leucogenys	ENSNLEG00000016894	1 retrocopy	retro_nleu_216,
Ictidomys tridecemlineatus	ENSSTOG00000004810	1 retrocopy	retro_itri_699,
Tupaia belangeri	ENSTBEG00000015052	2 retrocopies	retro_tbel_1277, retro_tbel_4083,