RetrogeneDB ID: retro_ptro_3211

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:47782205..47782646(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NICN1
• Ensembl ID: ENSPTRG00000032494
• Aliases: None
• Description: None

Sequence

>retro_ptro_3211
TCAGCACACACACCGGCCAAGTGGGTGACCTGCCTGTGGGACTACTGTCTGATGCCCGACCCACACAGTGAGGAGGGAGC
CCAGGAGTATGTGTCGCTGTTCAAGCAACAGATACTGTGTGACATGGCCAGAATATCGGAGCTACACCTGATTCTGCAGC
AGCCATCACCACTGTGGCTGTCTTTCACAGTGGAGGAGCTGCAGATCTATCAGCAGGGACCAAAGAGCCCCTCCATGATC
TTCCCCAAGTGGCTCTCCCACCCAGTGCCCTGTGAGCAACCTGCACTCCTCCATGAGGGTCTCCCAGACCCCAGCAGGGT
ATCCTCTGAGGTGCAGCAGATGTGGGCACTGACAGAGATGATCCGGGCCAGTCACACCTCCGCGAGGATAGGCCACTTTG
ATGTAGATGGCTGTTATGACCTGAACTTGCTCTCCTACACT

Alignment

ORF - retro_ptro_3211 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.2 %
• Parental protein coverage: 69.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAHTPAKWVTCLRDYCLMPDPHSEEGAQEYVSLFKHQMLCDMARVSELRLILRQPSPLWLSFTVEELQIY
          SAHTPAKWVTCL.DYCLMPDPHSEEGAQEYVSLFK.Q.LCDMAR.SEL.LIL.QPSPLWLSFTVEELQIY
Retrocopy SAHTPAKWVTCLWDYCLMPDPHSEEGAQEYVSLFKQQILCDMARISELHLILQQPSPLWLSFTVEELQIY

Parental  QQGPKSPSVTFPKWLSHPVPCEQPALLREGLPDPSRVSSEVQQMWALTEMIRASHTSARIGRFDVDGCYD
          QQGPKSPS..FPKWLSHPVPCEQPALL.EGLPDPSRVSSEVQQMWALTEMIRASHTSARIG.FDVDGCYD
Retrocopy QQGPKSPSMIFPKWLSHPVPCEQPALLHEGLPDPSRVSSEVQQMWALTEMIRASHTSARIGHFDVDGCYD

Parental  LNLLSYT
          LNLLSYT
Retrocopy LNLLSYT

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	25.86 RPM
SRP007412_cerebellum	0.00 RPM	18.86 RPM
SRP007412_heart	0.00 RPM	5.68 RPM
SRP007412_kidney	0.00 RPM	14.93 RPM
SRP007412_liver	0.00 RPM	5.11 RPM
SRP007412_testis	0.00 RPM	3.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3211 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3211 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4824

---

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 ,