RetrogeneDB ID: retro_ptro_2000

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:84029886..84030933(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039556
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDEL1
• Ensembl ID: ENSPTRG00000008744
• Aliases: None
• Description: NudE nuclear distribution gene E homolog-like 1 [Source:UniProtKB/TrEMBL;Acc:K7CHH7]

Sequence

>retro_ptro_2000
GCTTTCTTGATCATGGATGGTGAAGATATACCAGATTTTTCAAGTTTAAAGGAGGAAACTGCTTATTGGAAGGAACTTTC
CTTGAAGTATAAGCAAAGCTTCCAGGAAGCTCGGGATGAGCTAGTTGAATTCCAGGAAGGAAGCAGAGAATTAGAAGCAG
AGTTGGAGGCACAATTAGTACAGGCTGAACAAAGAAATAGAGACTTGCAGGCTGATAACCAAAGACTGAAATATGAAGTG
GAGGCATTAAAGGAGAAGCTAGAGCATCAATATGCACAGAGCTATAAGCAGGTCTCAGTGTTAGAAGATGATTTAAGTCA
GACTCGGGCCATTAAGGAGCAGTTGCATAAGTATGTGAGAGAGCTGGAGCAGGCCAACGACGACCTGGAGCGAGCCAAAA
GGGCAACAATAGTTTCACTGGAAGACTTTGAACAAAGGCTAAATCAGGCCATTGAACGAAATGCATTTTTAGAAAGTGAA
CTTGATGAAAAGGAATCTTTGTTGGTCTCTGTACAGAGGTTAAAGGATGAAGCAAGAGATTTAAGGCAAGAACTAGCAGT
TCGGGAAAGACAACAGGAAGTAACTAGAAAGTCGGCTCCTAGCTCTCCAACTCTAGACTGTGAAAAGATGGACTCCGCCG
TCCAAGCATCACTTTCTTTGCCAGCTACCCCTGTTGGCAAAGGAACGGAGAACACTTTTCCTTCACCGAAAGCTATACCA
AATGGTTTTGGTACCAGTCCACTAACTCCCTCTGCTAGGATATCAGCACTAAACATCGTGGGGGATCTCTTACAGAAAGT
AGGGGCTTTAGAATCCAAATTAGCAGCTTGCAGGAATTTTGCAAAGGACCAAGCATCACGAAAATCCTATATTTCAGGGA
ATGTTAACTGTGGGGTGCTGAATGGCAATGGCACAAAGTTCTCTCGATCAGGGCATACATCTTTCTTCGACAAAGGGGCA
GTAAACGGCTTTGACCCCACTCCTCCTCCTCCTGGTCTGGGCTCCTCGCATCCATCGTCAGTGCCGGGTATGCTGCCTCT
CAGTGTG

Alignment

ORF - retro_ptro_2000 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.85 %
• Parental protein coverage: 91.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFLIMDGEDIPDFSSLKEETAYWKELSLKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQ
          AFLIMDGEDIPDFSSLKEETAYWKELSLKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQ
Retrocopy AFLIMDGEDIPDFSSLKEETAYWKELSLKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQ

Parental  ADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSL
          ADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSL
Retrocopy ADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSL

Parental  EDFEQRLNQAIERNAFLESELDEKESLLVSVQRLKDEARDLRQELAVRERQQEVTRKSAPSSPTLDCEKM
          EDFEQRLNQAIERNAFLESELDEKESLLVSVQRLKDEARDLRQELAVRERQQEVTRKSAPSSPTLDCEKM
Retrocopy EDFEQRLNQAIERNAFLESELDEKESLLVSVQRLKDEARDLRQELAVRERQQEVTRKSAPSSPTLDCEKM

Parental  DSAVQASLSLPATPVGKGTENTFPSPKAIPNGFGTSPLTPSARISALNIVGDLLRKVGALESKLAACRNF
          DSAVQASLSLPATPVGKGTENTFPSPKAIPNGFGTSPLTPSARISALNIVGDLL.KVGALESKLAACRNF
Retrocopy DSAVQASLSLPATPVGKGTENTFPSPKAIPNGFGTSPLTPSARISALNIVGDLLQKVGALESKLAACRNF

Parental  AKDQASRKSYISGNVNCGVLNGNGTKFSRSGHTSFFDKGAVNGFDPAPPPPGLGSSRPSSAPGMLPLSV
          AKDQASRKSYISGNVNCGVLNGNGTKFSRSGHTSFFDKGAVNGFDP.PPPPGLGSS.PSS.PGMLPLSV
Retrocopy AKDQASRKSYISGNVNCGVLNGNGTKFSRSGHTSFFDKGAVNGFDPTPPPPGLGSSHPSSVPGMLPLSV

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	1.14 RPM	32.67 RPM
SRP007412_cerebellum	2.44 RPM	12.62 RPM
SRP007412_heart	0.55 RPM	3.35 RPM
SRP007412_kidney	0.44 RPM	4.55 RPM
SRP007412_liver	0.72 RPM	7.79 RPM
SRP007412_testis	1.16 RPM	6.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2000 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2000 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014341	1 retrocopy	retro_cjac_4072,
Cavia porcellus	ENSCPOG00000012878	1 retrocopy	retro_cpor_626,
Pan troglodytes	ENSPTRG00000008744	1 retrocopy	retro_ptro_2000 ,
Ictidomys tridecemlineatus	ENSSTOG00000027930	1 retrocopy	retro_itri_620,
Tursiops truncatus	ENSTTRG00000006517	1 retrocopy	retro_ttru_1239,