RetrogeneDB ID: retro_pabe_1195

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:74705370..74705771(-)
• Located in intron of: ENSPPYG00000005971

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C
• Ensembl ID: ENSPPYG00000008619
• Aliases: None
• Description: 5', 3'-nucleotidase, cytosolic [Source:HGNC Symbol;Acc:17144]

Sequence

>retro_pabe_1195
GGCCTCCTGCTGGGCTTCAGCCACTGCTTCTCAGGGAGCTGCATGTGACACTGCAGCAGCACCGCAGCTTCCTGGCCTGG
AAGCAGTACCGCACCCTGCTGCCGGACCTGGTGGATAAAGTGGCCCATGGGTGTGAAGCCCTAGGCTTTTCCCTAGTTCT
TGGAGCCCAACCCCGGAGGGTCTTCCAAGAGATGAAGCACATGCAAAACACCGAGGTCTTTATACTGCACCAGCCCCTGC
CAAAGTATGACCACTGTGTGGGTGAGAAGCACTGCTGGGTAGAGCAGCACCTGGAGCCCCAGCTTGTGGAGTGAATTATC
CTTACAATGGACAAGACCGTGGTCTTTGGGGACTTGCTTACTGATGACAAGGATACCATTCGAGGCCAAGAGGAGAGGCC
G

Alignment

ORF - retro_pabe_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.77 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLLRGFRRRFP-EEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMND
          GLL.GF...F...E.HV.L.Q.R.FLA..QYR.L.PDL.DKVA...EA.GF.L.L...P.......EM..
Retrocopy GLLLGFSHCFS<RELHVTLQQHRSFLAWKQYRTLLPDLVDKVAHGCEALGFSLVLGAQPRRV--FQEMKH

Parental  LPDTEVFICTSPLLKYDHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTIRGQEETP
          ...TEVFI...PL.KYDHCVGEK..WVEQHL.PQ.VE.IILT.DKTVV.GDLL.DDKDTIRGQEE.P
Retrocopy MQNTEVFILHQPLPKYDHCVGEKHCWVEQHLEPQLVE*IILTMDKTVVFGDLLTDDKDTIRGQEERP

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	0.06 RPM	0.00 RPM
SRP007412_cerebellum	0.12 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.13 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1195 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1195 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009175	1 retrocopy	retro_amel_1684,
Callithrix jacchus	ENSCJAG00000014578	1 retrocopy	retro_cjac_810,
Felis catus	ENSFCAG00000031408	2 retrocopies	retro_fcat_1016, retro_fcat_606,
Homo sapiens	ENSG00000125458	2 retrocopies	retro_hsap_1441, retro_hsap_1442,
Gorilla gorilla	ENSGGOG00000004740	2 retrocopies	retro_ggor_1061, retro_ggor_1109,
Microcebus murinus	ENSMICG00000017488	1 retrocopy	retro_mmur_1088,
Mustela putorius furo	ENSMPUG00000013985	1 retrocopy	retro_mputfur_1352,
Nomascus leucogenys	ENSNLEG00000000601	2 retrocopies	retro_nleu_1083, retro_nleu_1416,
Pongo abelii	ENSPPYG00000008619	1 retrocopy	retro_pabe_1195 ,