RetrogeneDB ID: retro_ptro_877

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:89103978..89104411(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL2
• Ensembl ID: ENSPTRG00000017396
• Aliases: None
• Description: GrpE protein homolog [Source:UniProtKB/TrEMBL;Acc:H2QRR7]

Sequence

>retro_ptro_877
TTGGCCGTGCAGTTGCTGTGGCAGATGCAGCCCCTACTGGCCTCGAGTGCTGAGTGGGAGGGCAAGGGATGGCTACTTCT
ATTCAGCACTGCCATGCAGAGAACTACTGGTGAGGACTGCAGTTCTGAGGACCCTCCTGATGAGCTTGGGTGCTCTCTTG
CTGAATGGGCCTTAAGGGTGAAAGCTGTTAAACTGGAGAAGGAAGTCCAGGATTTAACGATGAGATACCAGAGAGCTGTA
GCTGACTGTGAAAACATAAGGAGGGGAACCAGAGATGTGTGGAAAACTCCAAGATATTTAGAATCCAGAGTTTCTGTAAG
ATCTTGGTGGAGGTGTCCACATTTTGGAGAAGACTACAGAGTGCATTTCTGAAGAATCAGACCCTGTGGACCAGAAGCTC
ACTCTGGAGAAGGTCTTCCAAGGGTTGTCACTT

Alignment

ORF - retro_ptro_877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.5 %
• Parental protein coverage: 66.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVRSLWAGRLRVHRLLAWSAAWESKGWPLPFSTATQRTAGEDCRSEDPPDELGPPLAERALRVKAVKLE
          .AV..LW........LLA.SA.WE.KGW.L.FSTA.QRT.GEDC.SEDPPDELG..LAE.ALRVKAVKLE
Retrocopy LAVQLLW----QMQPLLASSAEWEGKGWLLLFSTAMQRTTGEDCSSEDPPDELGCSLAEWALRVKAVKLE

Parental  KEVQDLTVRYQRAIADCENIRRRT-QRCVEDAKIFGIQSFCKDLVEVA-DILEKTTECISEESEPEDQKL
          KEVQDLT.RYQRA.ADCENIRR.T.QRCVE..KIF.IQSFCK.LVEV...ILEKTTECISEES.P.DQKL
Retrocopy KEVQDLTMRYQRAVADCENIRRGT<QRCVENSKIFRIQSFCKILVEVS<HILEKTTECISEESDPVDQKL

Parental  TLEKVFRGLLL
          TLEKVF.GL.L
Retrocopy TLEKVFQGLSL

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	0.02 RPM	11.46 RPM
SRP007412_cerebellum	0.00 RPM	17.28 RPM
SRP007412_heart	0.00 RPM	9.56 RPM
SRP007412_kidney	0.03 RPM	10.93 RPM
SRP007412_liver	0.00 RPM	4.62 RPM
SRP007412_testis	0.00 RPM	13.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_877 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_877 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1284
Pongo abelii	retro_pabe_1063
Macaca mulatta	retro_mmul_1317

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004070	1 retrocopy	retro_chof_1984,
Dipodomys ordii	ENSDORG00000011142	1 retrocopy	retro_dord_353,
Felis catus	ENSFCAG00000003624	1 retrocopy	retro_fcat_618,
Homo sapiens	ENSG00000164284	2 retrocopies	retro_hsap_1284, retro_hsap_4842,
Gorilla gorilla	ENSGGOG00000005410	2 retrocopies	retro_ggor_1008, retro_ggor_3021,
Macaca mulatta	ENSMMUG00000021662	1 retrocopy	retro_mmul_1317,
Nomascus leucogenys	ENSNLEG00000010160	1 retrocopy	retro_nleu_710,
Oryctolagus cuniculus	ENSOCUG00000016138	3 retrocopies	retro_ocun_89, retro_ocun_905, retro_ocun_943,
Otolemur garnettii	ENSOGAG00000014326	1 retrocopy	retro_ogar_791,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544, retro_ptro_2633, retro_ptro_2636,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877 ,
Sorex araneus	ENSSARG00000005467	2 retrocopies	retro_sara_320, retro_sara_511,