RetrogeneDB ID: retro_btau_570

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:8367848..8368149(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: URM1
• Ensembl ID: ENSBTAG00000025612
• Aliases: None
• Description: Ubiquitin-related modifier 1 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q148F0]

Sequence

>retro_btau_570
ATGGCAGCGCCCTTTTCAGTGGAGGTGGAGTTCGGAGGTGGTGCGGAGCTCCTGTTTGGCGGTGTGAAGGAAGCATCAGG
TCACCTTGCCTGAACAGGAGGAACCCTGGGACATCCGCAGCCTCCTTGTGTGGATCAAGAATTTGCTAAAACAGCGGCCA
GAGCTGTTCATCCAAGGAGACAGCATGAGGCCAGGGATTCTGGTGCTGGTTAAAGATGCCGACTGGGAACTGCTGGGTGA
GCTGGACTACCAGCTTCAGGACCAAGATAGCGTCCTCTTCATCTCCACGCTGCATGACGGC

Alignment

ORF - retro_btau_570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPLSVEVEFGGGAELLFDGVK-KHQVTLPGQEEPWDIRSLLVWIKKNLLKERPELFIQGDSVRPGILV
          MAAP.SVEVEFGGGAELLF.GVK.KHQVTLP.QEEPWDIRSLLVWIK.NLLK.RPELFIQGDS.RPGILV
Retrocopy MAAPFSVEVEFGGGAELLFGGVK>KHQVTLPEQEEPWDIRSLLVWIK-NLLKQRPELFIQGDSMRPGILV

Parental  LVNDADWELLGELDYQLQDQDSVLFISTLHGG
          LV.DADWELLGELDYQLQDQDSVLFISTLH.G
Retrocopy LVKDADWELLGELDYQLQDQDSVLFISTLHDG

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	6.99 RPM
ERP005899_muscle	0.00 RPM	39.01 RPM
SRP017611_brain	0.00 RPM	21.83 RPM
SRP017611_kidney	0.06 RPM	23.95 RPM
SRP017611_liver	0.00 RPM	14.50 RPM
SRP030211_testis	0.00 RPM	19.88 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_570 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_570 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025612	2 retrocopies	retro_btau_1694, retro_btau_570 ,
Erinaceus europaeus	ENSEEUG00000012945	1 retrocopy	retro_eeur_458,
Loxodonta africana	ENSLAFG00000002178	1 retrocopy	retro_lafr_542,
Macropus eugenii	ENSMEUG00000014147	1 retrocopy	retro_meug_1161,