RetrogeneDB ID: retro_pabe_1063

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:90775650..90776085(-)
• 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_1063
TTGGCCGTGCAGTTGCTGTGGCAGATGCAGCCCCTACTGGCCTCGAGTGCCGAGTGGGAGGGCAAGGGATGGCTACTTCT
ATTCAGCACTGCCATCCAGAGAACTACTGGTGAGGACAGCAGTTCTGAGGATCCTCCTGATGAGCTTGGGTGCTCTCTTG
CTGAATGGGCCTTAAGGGTAAAAGCTGTTAAACTGGAGAAGGAAGTCCAGGATTTAATGATGAGATACCAGAAAGCTGTA
GCTGACTGTGAAAACATAAGGAGGGGAACCCAGAGATGTGTGGAAGACTCCAAGATATTTGGAATCCAGAGTTTCTGTAA
GATCTTGGTGGAGGTGTTCCACATTTTGGAGAAGACTACAGAGTGCATTTCTGAAGAATGAGAACCTGTGGACCAGAAGC
TCACTCTGGAGAAGGTCTTCCAAGGGTTGTCACTT

Alignment

ORF - retro_pabe_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.18 %
• Parental protein coverage: 66.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVRSLWACRLRVQRLLAWSAAWESKGWPLPFSTATQRTAGEDCRSEDPPDELGPPLAERALRVKAVKLE
          .AV..LW......Q.LLA.SA.WE.KGW.L.FSTA.QRT.GED..SEDPPDELG..LAE.ALRVKAVKLE
Retrocopy LAVQLLW----QMQPLLASSAEWEGKGWLLLFSTAIQRTTGEDSSSEDPPDELGCSLAEWALRVKAVKLE

Parental  KEVQDLTVRYQRAVADCENIRRRTQRCVEDAKIFGIQSFCKDLVEVADILEKTTECISEESEPEDQKLTL
          KEVQDL..RYQ.AVADCENIRR.TQRCVED.KIFGIQSFCK.LVEV..ILEKTTECISEE.EP.DQKLTL
Retrocopy KEVQDLMMRYQKAVADCENIRRGTQRCVEDSKIFGIQSFCKILVEVFHILEKTTECISEE*EPVDQKLTL

Parental  EKVFRGLLL
          EKVF.GL.L
Retrocopy EKVFQGLSL

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	0.12 RPM	15.81 RPM
SRP007412_heart	0.06 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_1063 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1063 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1063 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1284
Pan troglodytes	retro_ptro_877
Macaca mulatta	retro_mmul_1317

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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,