RetrogeneDB ID: retro_ptro_1242

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:73362096..73363108(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NR2F6
• Ensembl ID: ENSPTRG00000010661
• Aliases: None
• Description: nuclear receptor subfamily 2, group F, member 6 [Source:HGNC Symbol;Acc:7977]

Sequence

>retro_ptro_1242
CATTACGGTGTCTTCCCTGCGAGGGCTGCAAAAGCTTTTTTAGCGGAGCATCCGCCGCAACCTCAGCTACACCTGCCGGT
CCAACCGTGACTGCCAGATCGACCAGCACCACCGGAACCAGTGCCAGTACTGCCGTCTCAAGAAGTGCTTCCGGGTGGGC
ATGAGGAAGGAGGCGGTGCAGCGCGGCCGCATCCCGCACTCGCTGCCTGGTGCCGTGGCCGCCTCCTCGGGCAGCCCCCC
GGGCTCGGCGCTGGCGGCAGTGGCGAGCGGCGGAGACCTCTTCCCGGGGCAGCCGGTGTCCGAACTGATCGCGCAGCTGT
TGCGCGCTGAGCCCTACCCTGCGGCGGCCGGACGCTTCGGCGCAGGGGGCGGCGCGGCGGGCGCGGTGCTGGGCATCGAC
AACGTGTGCGAGCTGGCGGCGCGGCTGCTCTTCAGCACCGTGGAGTGGGCGCGCCACGCGCCCTTCTTCCCCGAGCTGCC
GGTGGCCGACCAGGTGGTGCTGCTGCGCCTGAGCTGGAGCGAGCTCTTCGTGCTGAACGCGGCGCAGGCGGCGCTGCCCC
TGCACACGGCGCCGCTACTGGCCGCCGCCGGCCTCCACGCCTTGCCTATGGCCGCCGAGCGCGCAGTGGCCTTCATGGAC
CAGGTGCGCGCTTTCCAGGAGCAGGTGGACAAGCTGGGCCGCCTGCAGGTCGACTCGGCCGAGTATGGCTGCCTCAAGGC
CATCGCGCTCTTCACGCCCGATGCCTGTGGCCTCTCAGACCCGGCCCACGTTGAGAGCCTGCAGGAGAAGGCGCAGGTGG
CCCTCACCGAGTATGTGCGGGCGCAGTACCCGTCCCAGCCCCAGCGCTTCGGGCGCCTGCTGCTGCGGCTCCCCGCCCTG
CGCGCGGTCCCTGCCTCCCTCATCTCCCAGCTGTTCTTCATGCGCCTGGTGGGGAAGACACCCATTGAGACACTGATCAG
AGACATGCTGCTGTCGGGGAGTACCTTCAACTGGCCCTACGGCTCGGGCCAG

Alignment

ORF - retro_ptro_1242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 89.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HYGVFT-CEGCKSFFK-RSIRRNLSYTCRSNRDCQIDQHHRNQCQYCRLKKCFRVGMRKEAVQRGRIPHS
          HYGVF..CEGCKSFF..RSIRRNLSYTCRSNRDCQIDQHHRNQCQYCRLKKCFRVGMRKEAVQRGRIPHS
Retrocopy HYGVFP<CEGCKSFFS<RSIRRNLSYTCRSNRDCQIDQHHRNQCQYCRLKKCFRVGMRKEAVQRGRIPHS

Parental  LPGAVAAASGSPPGSALAAVASGGDLFPGQPVSELIAQLLRAEPYPAAAGRFGAGGGAAGAVLGIDNVCE
          LPGAVAA.SGSPPGSALAAVASGGDLFPGQPVSELIAQLLRAEPYP................LGIDNVCE
Retrocopy LPGAVAASSGSPPGSALAAVASGGDLFPGQPVSELIAQLLRAEPYPXXXXXXXXXXXXXXXXLGIDNVCE

Parental  LAARLLFSTVEWARHAPFFPELPVADQVALLRLSWSELFVLNAAQAALPLHTAPLLAAAGLHAAPMAAER
          LAARLLFSTVEWARHAPFFPELPVADQV.LLRLSWSELFVLNAAQAALPLHTAPLLAAAGLHA.PMAAER
Retrocopy LAARLLFSTVEWARHAPFFPELPVADQVVLLRLSWSELFVLNAAQAALPLHTAPLLAAAGLHALPMAAER

Parental  AVAFMDQVRAFQEQVDKLGRLQVDSAEYGCLKAIALFTPDACGLSDPAHVESLQEKAQVALTEYVRAQYP
          AVAFMDQVRAFQEQVDKLGRLQVDSAEYGCLKAIALFTPDACGLSDPAHVESLQEKAQVALTEYVRAQYP
Retrocopy AVAFMDQVRAFQEQVDKLGRLQVDSAEYGCLKAIALFTPDACGLSDPAHVESLQEKAQVALTEYVRAQYP

Parental  SQPQRFGRLLLRLPALRAVPASLISQLFFMRLVGKTPIETLIRDMLLSGSTFNWPYGSGQ
          SQPQRFGRLLLRLPALRAVPASLISQLFFMRLVGKTPIETLIRDMLLSGSTFNWPYGSGQ
Retrocopy SQPQRFGRLLLRLPALRAVPASLISQLFFMRLVGKTPIETLIRDMLLSGSTFNWPYGSGQ

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	1.22 RPM	22.33 RPM
SRP007412_cerebellum	0.32 RPM	7.60 RPM
SRP007412_heart	0.17 RPM	5.19 RPM
SRP007412_kidney	0.94 RPM	28.85 RPM
SRP007412_liver	1.24 RPM	33.72 RPM
SRP007412_testis	0.00 RPM	2.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1242 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1242 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1242 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000010661	1 retrocopy	retro_ptro_1242 ,
Pan troglodytes	ENSPTRG00000020357	1 retrocopy	retro_ptro_869,