RetrogeneDB ID: retro_pabe_3337

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:61572338..61572663(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT15
• Ensembl ID: ENSPPYG00000005353
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 15 [Source:HGNC Symbol;Acc:23063]

Sequence

>retro_pabe_3337
TGTTTCCTTCTGGGGAAGAGAAAGGGGTCGTCTGGAGCCAGCAGTTTCCAACTTCCTGGGGGTCGTCTGGAGTTCGGTGA
GAGCTGGGAAGAATGCACTAAAAAGGAAGCCTGGAAAGAAGCAGCTCTTCACCTGAAAAATGTTTGCTTTGCCTCAGTTG
AGAATTGTTTCGTTGAGAAAGAGAATTATCATGTTACCATATTAACCAAAGGAGAGGTGGACGTGACTCATGATTCAGAA
TCACAGAATGTGGAGCCTGAAAAAAAATGAAAGTTGGAACTGGGTTCCTTGGGAAGAATTTCCTCTACTAGATCAGCTTT
TCTGG

Alignment

ORF - retro_pabe_3337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.36 %
• Parental protein coverage: 66.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVLLGKRKGSVGAGSFQLPGGHLEFGETWEECAQRETWEEAALHLKNVRFASVVNSFIEKENYHYVTVLM
          C.LLGKRKGS.GA.SFQLPGG.LEFGE.WEEC...E.W.EAALHLKNV.FASV.N.F.EKENYH.VT.L.
Retrocopy CFLLGKRKGSSGASSFQLPGGRLEFGESWEECTKKEAWKEAALHLKNVCFASVENCFVEKENYH-VTILT

Parental  KGEVDVTHDSEPKNVEP-EKNESWEWVPWEELPPLDQLFW
          KGEVDVTHDSE..NVEP....ESW.WVPWEE.P.LDQLFW
Retrocopy KGEVDVTHDSESQNVEP>XXXESWNWVPWEEFPLLDQLFW

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.35 RPM
SRP007412_cerebellum	0.00 RPM	6.69 RPM
SRP007412_heart	0.00 RPM	6.98 RPM
SRP007412_kidney	0.00 RPM	8.55 RPM
SRP007412_liver	0.00 RPM	3.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3337 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3337 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4063

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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,