RetrogeneDB ID: retro_pabe_3324

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:48971165..48971816(-)
• Located in intron of: ENSPPYG00000018571

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSFL1C
• Ensembl ID: ENSPPYG00000010851
• Aliases: None
• Description: NSFL1 cofactor p47 [Source:UniProtKB/Swiss-Prot;Acc:Q5RBG3]

Sequence

>retro_pabe_3324
GCAGCGGAGCAACAGGAGGCGCTGAGAAAGTTTGTGGCAGTGACGGGCACCGAGGAGGACCGGGCCTGCTTCTTCCTCGA
GTCAGCTACCTGGGACTTGCAGATTGCGCTAGTGAGCTTTTATGAGGACAGAGGGGAAGAAGACATCATAACCATTTAAC
AGGCAACCCCCAGTTCAGTGTCCAGAGGCACAGCCCCTAGTGATAATAGAGTGACATCCTTTAGAGACCTCACTCATGAC
CAAGATGAGGATGAGGAAGAGGAGGAAGGCTAGAGGTTTTATGCTGGGGCCTCAGAGAGAAGTGGACAGCAGATTGTTGG
CCCTCCCAGAAAGAAAAGTCCCAATGAGCTGGTGGATGATCTCTTTAAAGGTGCCAAAGAGCCTGGAGCTGTAGCTGTGG
AGCGAGTGACCAACAGACCTGGAGAGACCAGTACACCAAGACCATTTGCAGGAAGTGGCTATGGCCTTGGGGCAGCATCA
GAGGAAGAGTCTGCTTATGTGGCAGGAGAAAAGAGACAGCATTCCAGCCAAGATGTTCATGTAGTACTGAAACTCTGCAA
GAGTGGATTCAGCCTGGATAATGGAGAACTCAGAAGCTACTGAGACCCATCCGATGCCCAGTTTCTGGAGTCTATCCACA
GAAGGGAGGTG

Alignment

ORF - retro_pabe_3324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 58.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAERQEALREFVAVTGAEEDRARFFLESAGWDLQIALASFYEDGGDEDIVTISQATPSSVSRGTAPSDNR
          AAE.QEALR.FVAVTG.EEDRA.FFLESA.WDLQIAL.SFYED.G.EDI.TI.QATPSSVSRGTAPSDNR
Retrocopy AAEQQEALRKFVAVTGTEEDRACFFLESATWDLQIALVSFYEDRGEEDIITI*QATPSSVSRGTAPSDNR

Parental  VTSFRDLIHDQDEDEEEEEGQRFYAGGSERSGQQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSP
          VTSFRDL.HDQDEDEEEEEG.RFYAG.SERSGQQIVGPPRKKSPNELVDDLFKGAKE.GAVAVERVT..P
Retrocopy VTSFRDLTHDQDEDEEEEEG*RFYAGASERSGQQIVGPPRKKSPNELVDDLFKGAKEPGAVAVERVTNRP

Parental  GETSKPRPFAGGGYRLGAAPEEESAYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLE
          GETS.PRPFAG.GY.LGAA.EEESAYVAGEKRQHSSQDVHVVLKL.KSGFSLDNGELRSY.DPS.AQFLE
Retrocopy GETSTPRPFAGSGYGLGAASEEESAYVAGEKRQHSSQDVHVVLKLCKSGFSLDNGELRSY*DPSDAQFLE

Parental  SIRRGEV
          SI.R.EV
Retrocopy SIHRREV

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	0.28 RPM	74.48 RPM
SRP007412_cerebellum	0.36 RPM	47.91 RPM
SRP007412_heart	0.63 RPM	24.08 RPM
SRP007412_kidney	0.70 RPM	39.81 RPM
SRP007412_liver	0.95 RPM	36.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3324 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3324 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4050

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Macropus eugenii	ENSMEUG00000003940	2 retrocopies	retro_meug_1890, retro_meug_605,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565,
Nomascus leucogenys	ENSNLEG00000009341	1 retrocopy	retro_nleu_2800,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144, retro_ogar_1609,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324 ,
Pongo abelii	ENSPPYG00000018610	1 retrocopy	retro_pabe_3195,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,