RetrogeneDB ID: retro_btau_1336

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:116235288..116235510(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.49569
• Ensembl ID: ENSBTAG00000011893
• Aliases: None
• Description: Haloacid dehalogenase-like hydrolase domain-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCH9]

Sequence

>retro_btau_1336
ATGGAGGCATTGCGGGGCACTGGCTGTGAACCTGAGGAGACCGTTATGATTGGAGATGACTGCGGAGATGATGTTGGTGG
GGCTCAGAATGCTGGCATGCGGGACATCTTAGTCAAGACAGGGAAATATCGAGCACCAGACGAAGACAAAATTAACCCAG
CTCCTTACTTAACCTGTGAGAGCTTCCCACATGCCATGGACCACATTCTGGAGCATTTGCTG

Alignment

ORF - retro_btau_1336 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.89 %
• Parental protein coverage: 57.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEALRGTGCEPEETVMIGDDCRDDVGGAQNAGMRGILVKTGKYRAADEDKINPAPYLTCESFPHAVDHIL
          .EALRGTGCEPEETVMIGDDC.DDVGGAQNAGMR.ILVKTGKYRA.DEDKINPAPYLTCESFPHA.DHIL
Retrocopy MEALRGTGCEPEETVMIGDDCGDDVGGAQNAGMRDILVKTGKYRAPDEDKINPAPYLTCESFPHAMDHIL

Parental  QHLL
          .HLL
Retrocopy EHLL

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	9.59 RPM
ERP005899_muscle	0.00 RPM	14.57 RPM
SRP017611_brain	0.00 RPM	24.53 RPM
SRP017611_kidney	0.00 RPM	16.71 RPM
SRP017611_liver	0.00 RPM	8.23 RPM
SRP030211_testis	0.01 RPM	37.46 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1336 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1336 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011893	1 retrocopy	retro_btau_1336 ,
Choloepus hoffmanni	ENSCHOG00000009397	1 retrocopy	retro_chof_100,
Macaca mulatta	ENSMMUG00000010999	1 retrocopy	retro_mmul_595,
Ictidomys tridecemlineatus	ENSSTOG00000008527	1 retrocopy	retro_itri_55,