RetrogeneDB ID: retro_pabe_1490

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:27231405..27231789(-)
• 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_1490
ATGACAGCCAACATGGAGCCACAGGGGCGGCCGCCCAGAGTCAGAGTCTGAGTTGTGGTGACCAGCTGCAAGCATCCGTG
TTGTATCCTCCTGGGGAAGAGGAAAGGGTCGTTTGGAGCCAGCATTTTTCAGCTTTCTGGGGGTCATTTGGAGTTAACTG
AGAGCTGGGAAGAATGTGCTCAAAGGGAAACCTGGGAAGAAGCTCTTCACCTGAAAAATGTTCGCTTTGCCTCAGTTGTG
AACTCTTTCACTGAGAAGAATTACCATTATGTTACTGTATTAATGAAAGGAGAAGTGGACATGACTCATGATTCAGAACC
AAAGAATGTAGAGCCTGAAAAAAATGAAAGTTGGGAGTGGGTTCCCTGGGAACAATTTCCTCCT

Alignment

ORF - retro_pabe_1490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.54 %
• Parental protein coverage: 79.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTASGQLSGRRPGVGVGVVVTSCKHPRCVLLGKRKGSVGAGSFQLPGGHLEFGETWEECAQRETWEEAAL
          MTA.....GR.P.V.V.VVVTSCKHP.C.LLGKRKGS.GA..FQL.GGHLE..E.WEECAQRETWEEA.L
Retrocopy MTANMEPQGRPPRVRV*VVVTSCKHPCCILLGKRKGSFGASIFQLSGGHLELTESWEECAQRETWEEA-L

Parental  HLKNVRFASVVNSFIEKENYHYVTVLMKGEVDVTHDSEPKNVEPEKNESWEWVPWEELPP
          HLKNVRFASVVNSF.EK.NYHYVTVLMKGEVD.THDSEPKNVEPEKNESWEWVPWE..PP
Retrocopy HLKNVRFASVVNSFTEK-NYHYVTVLMKGEVDMTHDSEPKNVEPEKNESWEWVPWEQFPP

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	0.11 RPM	8.35 RPM
SRP007412_cerebellum	0.36 RPM	6.69 RPM
SRP007412_heart	0.21 RPM	6.98 RPM
SRP007412_kidney	0.03 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_1490 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1490 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1822
Gorilla gorilla	retro_ggor_2171

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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,