RetrogeneDB ID: retro_ptro_650

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:122786721..122787172(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF181
• Ensembl ID: ENSPTRG00000012138
• Aliases: None
• Description: None

Sequence

>retro_ptro_650
ATGACAGCCTATTTCAATGAACAAGACTGCAAGCTGTTGAACCCCAAGCAAGAGATCCTAACCCACATGCTGCTGGAGCT
CACCAGATCACTTTTCAATAGGATGGATTTTGAAGACTCGGGGATGGCAGTAAATTGGAATCACCACCTGCCTCCACCAG
CTGCCAAGACAGTGTGGTTGGGAACCTCCCCAGGACAGTCATCAGGAGCTCTCAGGCTGAGAGACACACACAAGTGCCCC
ATGTGCTTGAGGAGGAGGAGGCTGTTGTTGGGATGCCTTGCCATTAGCTTTTCCATTCTAACTGCATTTTGCCCCGGCTA
AGCAAGACAAATCCCTGTCCCTTGTGCTGCCAGGAGCTGCCCGCTGATAACGACACCTGTGAGGAGCACAGAGGAGACAA
GTCTCGAAACAGCAGCAGCAGCACTGTCTGGAGAACCTCTACAGAGCCATG

Alignment

ORF - retro_ptro_650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.94 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASYFDEHDCEPSDPEQETRTNMLLELARSLFNRMDFEDLGLVVDWDHHLP-PPAAK-TVVENLPRTVIR
          M..YF.E.DC....P.QE..T.MLLEL.RSLFNRMDFED.G..V.W.HHLP.P.A....VV.NLPRTVIR
Retrocopy MTAYFNEQDCKLLNPKQEILTHMLLELTRSLFNRMDFEDSGMAVNWNHHLPPPAAKT<SVVGNLPRTVIR

Parental  GSQAELKCPVCLLEFEEEETAIEMPCHHLFHSSCILPWLSKTNSCPLCRHELPTDDDTYEEHRRDKAR-K
          .SQAE....V.....EEEE....MPCH.LFHS.CILP.LSKTN.CPLC..ELP.D.DT.EEHR.DK.R.K
Retrocopy SSQAERHTQVPHV-LEEEEAVVGMPCH*LFHSNCILPRLSKTNPCPLCCQELPADNDTCEEHRGDKSR<K

Parental  QQQQHRLENLHGAM
          QQQQH.LENL..AM
Retrocopy QQQQHCLENLYRAM

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	0.57 RPM	25.42 RPM
SRP007412_cerebellum	0.29 RPM	21.87 RPM
SRP007412_heart	0.12 RPM	16.58 RPM
SRP007412_kidney	0.44 RPM	77.91 RPM
SRP007412_liver	0.20 RPM	44.22 RPM
SRP007412_testis	1.05 RPM	51.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_650 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_650 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_938
Gorilla gorilla	retro_ggor_759
Pongo abelii	retro_pabe_807
Macaca mulatta	retro_mmul_1128

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019647	3 retrocopies	retro_cjac_2423, retro_cjac_355, retro_cjac_3849,
Homo sapiens	ENSG00000168894	3 retrocopies	retro_hsap_1005, retro_hsap_3771, retro_hsap_938,
Macaca mulatta	ENSMMUG00000017824	3 retrocopies	retro_mmul_1128, retro_mmul_1637, retro_mmul_808,
Pongo abelii	ENSPPYG00000012225	2 retrocopies	retro_pabe_3083, retro_pabe_807,
Pan troglodytes	ENSPTRG00000012138	2 retrocopies	retro_ptro_2557, retro_ptro_650 ,