RetrogeneDB ID: retro_btau_1353

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:72574391..72574868(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000024334
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000038931
• Aliases: None
• Description: thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1-like [Source:RefSeq peptide;Acc:NP_001103564]

Sequence

>retro_btau_1353
ATGGTGCTGCAGCGCCTGCTGCCCTGGAGTACTTGCTGGACGATCTTTGGGTCTGCGGAGGCTGCGCTCTGGGGTTTGAA
GTCAATAAAAAGAAGCTGCCTCAGTTTTTGTACTGCTATTTGTGAAGGTGTCACTTATAAGGAGCTTAAAAACCTCCTGA
AGTCTAAAAAAATTATGTTAATTGATGTTAGAGAGCCATGGGAAATTTATGAGTCTGGAAAAATCCCTGGGTCTGTCAAT
ATACCATTGGATGATGTAGGTGAAGCTCTACAGATGAACCCAAAGGACTTCAAAGAGAACTACAAAGAAGTAAAGCCATC
CAAATCTGACAGTCTAGTGTTCTCTTGTTTAGCTGGAGTGAGAAGCAAGGTGGCTATGGTCACAGCAATATCTCTGGGCT
TTAACAATGCTCAACACTATGCTGGAGGATGGAAGGAATGGGCAACCTATGAACTTTCAGAGAAGAAACAAGGAAAT

Alignment

ORF - retro_btau_1353 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLQRLLPWSTCRTIFGSAEAVLWGLKSIKRSCLNFCTAICEGVTYKELKNLLKSKKIMLIDVREPWEIY
          MVLQRLLPWSTC.TIFGSAEA.LWGLKSIKRSCL.FCTAICEGVTYKELKNLLKSKKIMLIDVREPWEIY
Retrocopy MVLQRLLPWSTCWTIFGSAEAALWGLKSIKRSCLSFCTAICEGVTYKELKNLLKSKKIMLIDVREPWEIY

Parental  ESGKIPGSVNIPLDDVGEALQMNPKDFKEKYKEVKPSKSDSLVFSCLAGVRSKVAMVTAISLGFNNAQHY
          ESGKIPGSVNIPLDDVGEALQMNPKDFKE.YKEVKPSKSDSLVFSCLAGVRSKVAMVTAISLGFNNAQHY
Retrocopy ESGKIPGSVNIPLDDVGEALQMNPKDFKENYKEVKPSKSDSLVFSCLAGVRSKVAMVTAISLGFNNAQHY

Parental  AGGWKEWATYEISEKKQGN
          AGGWKEWATYE.SEKKQGN
Retrocopy AGGWKEWATYELSEKKQGN

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	2.52 RPM
ERP005899_muscle	0.16 RPM	10.29 RPM
SRP017611_brain	0.05 RPM	1.23 RPM
SRP017611_kidney	0.00 RPM	6.99 RPM
SRP017611_liver	0.00 RPM	1.06 RPM
SRP030211_testis	0.05 RPM	5.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1353 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1353 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008959	1 retrocopy	retro_amel_1055,
Bos taurus	ENSBTAG00000038931	1 retrocopy	retro_btau_1353 ,
Canis familiaris	ENSCAFG00000030791	1 retrocopy	retro_cfam_606,
Callithrix jacchus	ENSCJAG00000031571	1 retrocopy	retro_cjac_1967,
Equus caballus	ENSECAG00000024361	1 retrocopy	retro_ecab_791,
Gorilla gorilla	ENSGGOG00000022586	1 retrocopy	retro_ggor_1345,
Otolemur garnettii	ENSOGAG00000025707	2 retrocopies	retro_ogar_2601, retro_ogar_527,