RetrogeneDB ID: retro_pabe_3764

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:62034977..62035651(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL2
• Ensembl ID: ENSPPYG00000015933
• Aliases: None
• Description: grpE protein homolog 2, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001127040]

Sequence

>retro_pabe_3764
ATGGCCATGTGGTCGATGTGGGCGGGCCACCAGCAGGTGTAGCACCTACTGGCCTAGAGTGCCTCATGGGAGAGCAAGGG
ATGCCCACTTCCATTCAGCACTGCCACCCAGGGAACCGCTGGTGAGGACTGCCATTCCGAGGAGCCTCCTGATGAGCTTG
GGCCATCTCTTGCTGAACAAGACTTAAGGGTAAAAGCTGTTAAACTGGAGAAGGAAGTGCAGGATTTAATGGTGAGATAC
CAGAGAGCTATAGCTGATTCTGAAAACATAAGGAGGTGAACCCAGAGATGTGTGGAAGATGCCAAGATATTTGGAATCCA
GAGTTTCTGTAAGGACTTAGTGGAGGTGGCTGACATTTTGGAGAAGACTACAGAGTGCATTTCTGAAGAATCAGAGCCTG
GGGACCAGAAGCTCACTCTGGAGAAAGTCTTCCAACGGTTGTTACTTTTAGAAGCAAAGCTGAAAAGTGTGTTTGCCAAG
CATGACCTTGAGAAGCTGACACCCATTGGTGACAAATATGATTCCCATGAGCATGAATCCTCTGCATTGTGCCAGCTGGT
GTTGTGGTGCAGTCTGGCACCATGGCATTAATGAGACAAGATGGTTACAAACTTCATGGCTGGACCATTAGACTTGCCCA
GGTAGAAGTGACAGGTGAGTCTCAGAGAGGACTG

Alignment

ORF - retro_pabe_3764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVRSLWACRLRVQRLLAWSAAWESKGWPLPFSTATQRTAGEDCRSEDPPDELGPPLAERALRVKAVKLE
          MA..S.WA....V..LLA.SA.WESKG.PLPFSTATQ.TAGEDC.SE.PPDELGP.LAE..LRVKAVKLE
Retrocopy MAMWSMWAGHQQV*HLLA*SASWESKGCPLPFSTATQGTAGEDCHSEEPPDELGPSLAEQDLRVKAVKLE

Parental  KEVQDLTVRYQRAVADCENIRRRTQRCVEDAKIFGIQSFCKDLVEVADILEKTTECISEESEPEDQKLTL
          KEVQDL.VRYQRA.AD.ENIRR.TQRCVEDAKIFGIQSFCKDLVEVADILEKTTECISEESEP.DQKLTL
Retrocopy KEVQDLMVRYQRAIADSENIRR*TQRCVEDAKIFGIQSFCKDLVEVADILEKTTECISEESEPGDQKLTL

Parental  EKVFRGLLLLEAKLKSVFAKHGLEKLTPIGDKYDPHEHE-LICHVPAGVGVQPGTVALVRQDGYKLHGRT
          EKVF..LLLLEAKLKSVFAKH.LEKLTPIGDKYD.HEHE...C.VPAGV.VQ.GT.AL.RQDGYKLHG.T
Retrocopy EKVFQRLLLLEAKLKSVFAKHDLEKLTPIGDKYDSHEHE<ILCIVPAGVVVQSGTMALMRQDGYKLHGWT

Parental  IRLAQVEVAVESQRRL
          IRLAQVEV..ESQR.L
Retrocopy IRLAQVEVTGESQRGL

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	0.00 RPM	10.23 RPM
SRP007412_cerebellum	0.00 RPM	15.81 RPM
SRP007412_heart	0.00 RPM	8.61 RPM
SRP007412_kidney	0.00 RPM	6.46 RPM
SRP007412_liver	0.00 RPM	5.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3764 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3764 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4842
Pan troglodytes	retro_ptro_3226
Gorilla gorilla	retro_ggor_3021

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 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	ENSPPYG00000014573	1 retrocopy	retro_pabe_3235,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764 ,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877,
Sorex araneus	ENSSARG00000005467	2 retrocopies	retro_sara_320, retro_sara_511,