RetrogeneDB ID: retro_ptro_2455

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:92119271..92120522(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041986
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STK17A
• Ensembl ID: ENSPTRG00000019124
• Aliases: None
• Description: None

Sequence

>retro_ptro_2455
ATGATCCCTTTGGAGAAGCCAGGCAGCGGCGGCTCCTCCCCAGGCGCCACCTCAGGCTCGGGCCGGGCAGGCCGGGGTCT
GAGCGGGCCGTGCGGGCCGTGCCGGCTGCCGCCGCCGCCCCAGGCCCGCGGGCTGCTGACAGAGATACGCGCCGTGGTGC
GCACCGAGCCCTTCCAGGACGGCTACAGCCTGTGCCCGGGCCGGGAGCTGGGCAGGGGGAAATTTGCAGTGGTGAGAAAA
TGTATAAAGAAAGATTCTGGGAAAGAATTTGCTGCAAAGTTCATGAGAAAAAGAAGAAAAGGCCAAGATTGTCGGATGGA
AATAATTCATGAGACTGCTGTACTTGAACTAGCACAAGACAATCCTTGGGTCATTAATTTACATGAAGTTTATGAGACTG
CATCAGAAATGATCTTAGTTCTGGAATATGCTGCTGGGGGTGAAATCTTTGACCAGTGTGTTGCAGACAGAGAAGAAGCC
TTTAAAGAAAAAGATGTTCAAAGACTTATGCGACAGATTTTAGAAGGTGTTCACTTTTTACACACTCATGATGTAGTTCA
TCTTGATTTGAAGCCTCAGAATATTCTGTTGACAAGTGAATCTCCATTGGGTGACATTAAGATTGTTGATTTTGGCCTTT
CAAGAATATTGAAGAACAGTGAAGAGCTCCGAGAAATTATGGGTACCCCTGAATATGTGGCTCCTGAAATTCTTAGTTAT
GATCCTATAAGCATGGCAACAGATATGTGGAGCATTGGAGTGTTAACATATGTCATGCTTACAGGAATATCACCTTTCTT
AGGCAATGATAAACAAGAAACATTCTTAAACATCTCACAGATGAATTTAAGTTATTCTGAGGAAGAATTTGATGTTTTGT
CTGAGTCGGCTGTTGATTTCATCAGGACACTTTTAGTTAAGAAACCTGAAGATCGAGCCACTGCTGAAGAATGTCTAAAG
CACCCCTGGTTGACACAGAGCAGTATTCAAGAGCCTTCTTTCAGGATGGAAAAGGCACTAGAAGAAGCAAATGCCCTCCA
AGAAGGTCATTCTGTGCCTGAAATTAATTCAGATACCGACAAATCAGAAACCGAGGAATCCATTGTAACCGAAGAGTTAA
TTGTAGTTACTTCATATACTCTAGGACAATGCAGACAGTCTGAAAAAGAGAAAATGGAGCAAAAGGCCATTTCCAAACGA
TTTAAATTTGAGGAACCTTTGCTACAAGAAATTCCAGGAGAATTTATCTAC

Alignment

ORF - retro_ptro_2455 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIPLEKPGSGGSSPGATSGS---GRAGRGLSGPCRPPPPPQARGLLTEIRAVVRTEPFQDGYSLCPGREL
          MIPLEKPGSGGSSPGATSGS...GR...........PPPPQARGLLTEIRAVVRTEPFQDGYSLCPGREL
Retrocopy MIPLEKPGSGGSSPGATSGSGRAGRGLXXXXXXXXXPPPPQARGLLTEIRAVVRTEPFQDGYSLCPGREL

Parental  GRGKFAVVRKCIKKDSGKEFAAKFMRKRRKGQDCRMEIIHEIAVLEIAQDNPWVINLHEVYETASEMILV
          GRGKFAVVRKCIKKDSGKEFAAKFMRKRRKGQDCRMEIIHE.AVLE.AQDNPWVINLHEVYETASEMILV
Retrocopy GRGKFAVVRKCIKKDSGKEFAAKFMRKRRKGQDCRMEIIHETAVLELAQDNPWVINLHEVYETASEMILV

Parental  LEYAAGGEIFDQCVADREEAFKEKDVQRLMRQILEGVHFLHTRDVVHLDLKPQNILLTSESPLGDIKIVD
          LEYAAGGEIFDQCVADREEAFKEKDVQRLMRQILEGVHFLHT.DVVHLDLKPQNILLTSESPLGDIKIVD
Retrocopy LEYAAGGEIFDQCVADREEAFKEKDVQRLMRQILEGVHFLHTHDVVHLDLKPQNILLTSESPLGDIKIVD

Parental  FGLSRILKNSEELREIMGTPEYVAPEILSYDPISMATDMWSIGVLTYVMLTGISPFLGNDKQETFLNISQ
          FGLSRILKNSEELREIMGTPEYVAPEILSYDPISMATDMWSIGVLTYVMLTGISPFLGNDKQETFLNISQ
Retrocopy FGLSRILKNSEELREIMGTPEYVAPEILSYDPISMATDMWSIGVLTYVMLTGISPFLGNDKQETFLNISQ

Parental  MNLSYSEEEFDVLSESAVDFIRTLLVKKPEDRATAEECLKHPWLTQSSIQEPSFRMEKALEEANALQEGH
          MNLSYSEEEFDVLSESAVDFIRTLLVKKPEDRATAEECLKHPWLTQSSIQEPSFRMEKALEEANALQEGH
Retrocopy MNLSYSEEEFDVLSESAVDFIRTLLVKKPEDRATAEECLKHPWLTQSSIQEPSFRMEKALEEANALQEGH

Parental  SVPEINSDTDKSETEESIVTEELIVVTSYTLGQCRQSEKEKMEQKAISKRFKFEEPLLQEIPGEFIY
          SVPEINSDTDKSETEESIVTEELIVVTSYTLGQCRQSEKEKMEQKAISKRFKFEEPLLQEIPGEFIY
Retrocopy SVPEINSDTDKSETEESIVTEELIVVTSYTLGQCRQSEKEKMEQKAISKRFKFEEPLLQEIPGEFIY

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	0.04 RPM	5.13 RPM
SRP007412_cerebellum	0.00 RPM	4.70 RPM
SRP007412_heart	0.00 RPM	1.81 RPM
SRP007412_kidney	0.03 RPM	2.33 RPM
SRP007412_liver	0.03 RPM	2.09 RPM
SRP007412_testis	0.42 RPM	31.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2455 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2455 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000019124	1 retrocopy	retro_ptro_2455 ,