RetrogeneDB ID: retro_btau_559

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:40529975..40530379(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047574
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT15
• Ensembl ID: ENSBTAG00000019501
• Aliases: None
• Description: None

Sequence

>retro_btau_559
GGAGGAGGAGGAGCCATCGGTTTCCAACTTCCTGGGGGTCACTTGGAGTTCGGTGAAAGCTGGGAAGAATGTGCTTAAAA
GGAAACCTGGGAAGAAGGAGCTCTTCACCTGAAAAATGTTCACTTGGTCTTGGTTGTGAATTCTTTTGTTGAGAAAGAGA
ATTACCATTTGTCACTATTTTAATGAAAGGAGAGGTGGACCTGACTCATGATTTAGAACCAAAGAATGCAGAGCCTGAAA
AGAATGAAAGTTGGGAGTGGGTTCCTTGGAAAGAATTTCCTCCTCTGGACCAGCTTTTCTCGGCACTACGTTGTTTAAAG
GAACAAGGCTATGATCCTTTTAAATATTTGGATCATCTGGTAAGATATAAAGGAAGTCACCTAGAGGTGAACAAGGAGAC
TCAC

Alignment

ORF - retro_btau_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.48 %
• Parental protein coverage: 79.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSFGAGSFQLPGGHLEFGETWEECAQRETWEEAALHLKNVRFASVVNSFIEKENYH-YVTILMKGEVDLT
          G..GA..FQLPGGHLEFGE.WEECA..ETWEE.ALHLKNV....VVNSF.EKENYH..VTILMKGEVDLT
Retrocopy GGGGAIGFQLPGGHLEFGESWEECA*KETWEEGALHLKNVHLVLVVNSFVEKENYH<FVTILMKGEVDLT

Parental  HDSEPKNVEPEKNESWEWVPWEEFPPLDQLFWGLRCLKEQGYDPFKEDLDHLVGYKGSHLEVNKEIH
          HD.EPKN.EPEKNESWEWVPW.EFPPLDQLF..LRCLKEQGYDPFK..LDHLV.YKGSHLEVNKE.H
Retrocopy HDLEPKNAEPEKNESWEWVPWKEFPPLDQLFSALRCLKEQGYDPFKY-LDHLVRYKGSHLEVNKETH

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	3.82 RPM
ERP005899_muscle	0.00 RPM	3.64 RPM
SRP017611_brain	0.00 RPM	3.52 RPM
SRP017611_kidney	0.00 RPM	7.53 RPM
SRP017611_liver	0.00 RPM	8.00 RPM
SRP030211_testis	0.08 RPM	8.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_559 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_559 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019501	1 retrocopy	retro_btau_559 ,
Callithrix jacchus	ENSCJAG00000009274	1 retrocopy	retro_cjac_1497,
Homo sapiens	ENSG00000136159	2 retrocopies	retro_hsap_1822, retro_hsap_4063,
Gorilla gorilla	ENSGGOG00000008232	3 retrocopies	retro_ggor_2171, retro_ggor_2257, retro_ggor_2729,
Microcebus murinus	ENSMICG00000009583	1 retrocopy	retro_mmur_962,
Mus musculus	ENSMUSG00000033405	1 retrocopy	retro_mmus_1923,
Nomascus leucogenys	ENSNLEG00000002957	2 retrocopies	retro_nleu_2878, retro_nleu_563,
Pongo abelii	ENSPPYG00000005353	2 retrocopies	retro_pabe_1490, retro_pabe_3337,
Pan troglodytes	ENSPTRG00000042329	1 retrocopy	retro_ptro_82,
Tarsius syrichta	ENSTSYG00000006960	1 retrocopy	retro_tsyr_146,