RetrogeneDB ID: retro_pabe_3751

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:48061618..48062100(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NICN1
• Ensembl ID: ENSPPYG00000029914
• Aliases: None
• Description: nicolin 1 [Source:HGNC Symbol;Acc:18317]

Sequence

>retro_pabe_3751
TACTACACAGCTTTTTTGAGCATCCGTGTCTGTCAGCACACCTCAGCACACACACTGGCCAAGTGGGTGACCTGCCTGTG
GGACTACTGTCTGATGCCCGACCCACACAGTGAGGAAGGAGCCAGGAGTATGTGTCGCTGTTCAAGCAACAGATACTGTG
TGACATGGCCAGAGTATCGGAGCTACACCTGATTCTGCGGCAGCCATAACCACTGTGGCTGTCTTTCACAGTGGAGGAGC
TGCAGATCTATCAGCAGGGACCAAAGAGCCCCTCCATGATCTTCCCCAAGTGGCTCTCCCACCCAGTGCCCTGTGAGCAA
CCTGCACCCCTCCACGAGGGTTTCCCAGACCCCAGCAGGGTATCCTCTGAGGTGCAGCAGATGTGGGCACTGATAGAGAT
GATCCGGGCCAGTCACACCTCCGCGAGGATCGGCCACTTTTATGTAGATGGCTGTTATGACCTGAACTTGCTCTCCTACA
CT

Alignment

ORF - retro_pabe_3751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 75.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YYTAFLSIRVRQHTSAHTPAKWVTCLRDYCLMPDPHSEEGA-QEYVSLFKHQMLCDMARISELRLILRQP
          YYTAFLSIRV.QHTSAHT.AKWVTCL.DYCLMPDPHSEEGA.QEYVSLFK.Q.LCDMAR.SEL.LILRQP
Retrocopy YYTAFLSIRVCQHTSAHTLAKWVTCLWDYCLMPDPHSEEGA<QEYVSLFKQQILCDMARVSELHLILRQP

Parental  SPLWLSFTVEELQIYQQGPKSPSVTFPKWLSHPVPCEQPALLREGLPDPSRVSSEVQQMWALTEMIRASH
          .PLWLSFTVEELQIYQQGPKSPS..FPKWLSHPVPCEQPA.L.EG.PDPSRVSSEVQQMWAL.EMIRASH
Retrocopy *PLWLSFTVEELQIYQQGPKSPSMIFPKWLSHPVPCEQPAPLHEGFPDPSRVSSEVQQMWALIEMIRASH

Parental  TSTRIGRFDVDGCYDLNLLSYT
          TS.RIG.F.VDGCYDLNLLSYT
Retrocopy TSARIGHFYVDGCYDLNLLSYT

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	18.47 RPM
SRP007412_cerebellum	0.00 RPM	10.58 RPM
SRP007412_heart	0.00 RPM	5.30 RPM
SRP007412_kidney	0.00 RPM	11.97 RPM
SRP007412_liver	0.00 RPM	4.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3751 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3751 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3751 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145029	1 retrocopy	retro_hsap_4824,
Nomascus leucogenys	ENSNLEG00000006851	1 retrocopy	retro_nleu_2199,
Pongo abelii	ENSPPYG00000029914	1 retrocopy	retro_pabe_3751 ,
Pan troglodytes	ENSPTRG00000032494	1 retrocopy	retro_ptro_3211,