RetrogeneDB ID: retro_ptro_2557

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:107025645..107026105(+)
• 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_2557
ATGGCGTCCTATATCGATGAACACGACTGTGAGCCGTTGGACCCTCAAGCAGGAGACTCGAACCAACATGGTGCTGGAGC
TCGTAAGGTCACTTTTGAATAGGATGGACTTTGAAGACTTGGGGTTGGTAGTAGATTGGGACCACCACCTGCCTCCACCA
GCTGCCAAGATTGTGGTTGAGAACCTCTCCAGGACAGTCATCAGAGGCTCTCAAGGCTGAGCTCAAGTGCCCCGTTTATC
TTTTGGAATCTGAGGAGGAGACTGCCATTGAGATGCTTCCCATCACCTTTTTCATTCCAGCTGCATTCTGCCCTGGCTAA
GCAAGACAAATTCCTGTCCCTTGTGCCGCCATGAGCTGCCCACTGATGACTACACTTATGAGGAACACAGACGAGATAAG
GCTCGAAAACAGCAGCAGCAGCAGAACCGACTGGAGAACCTCCATGGAGCCATGTACACG

Alignment

ORF - retro_ptro_2557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASYFDEHDCEPSDPE-QETRTNMLLELARSLFNRMDFEDLGLVVDWDHHLPPPAAKTVVENLPRTVIRG
          MASY.DEHDCEP.DP..QETRTNM.LEL.RSL.NRMDFEDLGLVVDWDHHLPPPAAK.VVENL.RTVIRG
Retrocopy MASYIDEHDCEPLDPQ>QETRTNMVLELVRSLLNRMDFEDLGLVVDWDHHLPPPAAKIVVENLSRTVIRG

Parental  SQ-AELKCPVCLLEFEEEETAIEM-PCHHLFHSSCILPWLSKTNSCPLCRHELPTDDDTYEEHRRDKARK
          SQ.AELKCPV.LLE..EEETAIEM...HHLFHSSCILPWLSKTNSCPLCRHELPTDD.TYEEHRRDKARK
Retrocopy SQ>AELKCPVYLLE-SEEETAIEM<ASHHLFHSSCILPWLSKTNSCPLCRHELPTDDYTYEEHRRDKARK

Parental  -QQQQHRLENLHGAMYT
          .QQQQ.RLENLHGAMYT
Retrocopy QQQQQNRLENLHGAMYT

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	0.13 RPM	25.42 RPM
SRP007412_cerebellum	0.00 RPM	21.87 RPM
SRP007412_heart	0.06 RPM	16.58 RPM
SRP007412_kidney	0.08 RPM	77.91 RPM
SRP007412_liver	0.07 RPM	44.22 RPM
SRP007412_testis	0.21 RPM	51.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2557 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2557 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3771
Gorilla gorilla	retro_ggor_2537
Pongo abelii	retro_pabe_3083
Macaca mulatta	retro_mmul_1637

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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,