RetrogeneDB ID: retro_ptro_2518

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:31929800..31930718(+)
• Located in intron of: ENSPTRG00000019069

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB3IL1
• Ensembl ID: ENSPTRG00000003755
• Aliases: None
• Description: RAB3A interacting protein (rabin3)-like 1 [Source:HGNC Symbol;Acc:9780]

Sequence

>retro_ptro_2518
TCCATAGGAATTCACAAGAAGGGCTCTGAGCTCCTGAAGGAGAAGCTGCACAAAGCTCACAAGGAGCTGCAGCTGAAGGG
CGAAGACTGTGAGCAGCTGTTCCTAGTGCAGGAGCAGCTGCACAGGAGCTGGAGGAGCTGATGACTAGCCTATTTGAGGA
AGCCCACAAGATGGTGTGGGAAGCCAGCATACAGCAGGCAGTGTCAGAAAAGCAGCTGAATGCGGAGGCATGGGGAAAGA
TAGGCATGCTGCAGGCAGAGGTGACAGCTTGAAGACACTGGTCATCATGTCCACACCAGCCTCTCCCAACTACAAGCTCC
ACCTGCACCTGCTGAGCCCCACTAAGGGTGGGCCCTGCAAGGCCCACTGCCAACCTAAGAGCACCAGCAGTGCCCTCTCC
TTGGCCTTGTGACCCACCGTGAGACATGCCCTCACCTTGGACAAGGAGGTGGATGTGACACTATTGGCAGAGTTCCAAGC
CTGGAAGGAATTACCCACCTTGGACAAGACCTGTTCCTTGCTGCAAAGGGTGTAGTGGGAGGATATGGACCCCTGCCTGG
ACTTCACAGTGCAGAATCTCTTGCCACAGGTGTAGGCCTCTATGGGGGACACCACACTCACCATCAAGACTGTGGCTCTG
CAGAAGCTGCCTATGGTGAGGGTAACTGTGGTCAATTGTGGCAGTGCCAATATATGTGTCTTGAGCAATTTGGCCCATAC
CTGCCACCACCACCACATCTGGCTTTGTGACTTTGCAAGACACTACCACATCTCACTGTCTTCTCAGGCCAGGATCACTG
CAGTGTACAACTTTTTCATCTATATCTGCTACATCCACAAGGCCTGGTGCAACAGGATTTGAAGCCAGTGTTCTGGGAGA
TCACAAAGCTGTGAAAAGAGATACAGCTGGCCAAACTC

Alignment

ORF - retro_ptro_2518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.94 %
• Parental protein coverage: 75.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SMEIREKGSEFLKEELHRAQKELKLKDEECERLSKVREQLE-QELEELTASLFEEAHKMVREANMKQAAS
          S..I..KGSE.LKE.LH.A.KEL.LK.E.CE.L..V.EQL..QELEEL..SLFEEAHKMV.EA...QA.S
Retrocopy SIGIHKKGSELLKEKLHKAHKELQLKGEDCEQLFLVQEQLH<QELEELMTSLFEEAHKMVWEASIQQAVS

Parental  EKQLK-EARGKIDMLQAEVTA-LKTLVITSTPASPNRELHPQLLSPTKAGPRKGHSRHKSTSSTLCPAVC
          EKQL..EA.GKI.MLQAEVTA.LKTLVI.STPASPN..LH..LLSPTK.GP.K.H...KSTSS.L..A..
Retrocopy EKQLNAEAWGKIGMLQAEVTA<LKTLVIMSTPASPNYKLHLHLLSPTKGGPCKAHCQPKSTSSALSLAL*

Parental  PAAGHTLTPDREGKEVDTILFAEFQAWRESPTLDKTCPFLERVYREDVGPCLDFTMQELSVLVRAAVEDN
          P...H.LT.D...KEVD..L.AEFQAW.E.PTLDKTC..L.RV..ED..PCLDFT.Q.L...V.A...D.
Retrocopy PTVRHALTLD---KEVDVTLLAEFQAWKELPTLDKTCSLLQRV*WEDMDPCLDFTVQNLLPQV*ASMGDT

Parental  TLTIEPVASQTLPTVKVAEVDCSSTNTCALSGLTRTC-RHRIRLGDSKSHYYISPSSRARITAVCNFFTY
          TLTI..VA.Q.LP.V.V..V.C.S.N.C.LS.L..TC..H.I.L.D...HY.IS.SS.ARITAV.NFF.Y
Retrocopy TLTIKTVALQKLPMVRVTVVNCGSANICVLSNLAHTCHHHHIWLCDFARHYHISLSSQARITAVYNFFIY

Parental  IRYIQ-QGLVRQDAEPMFWEIMRLRKEMSLAKL
          I.YI..QGLV.QD..P.FWEI..L.KE..LAKL
Retrocopy ICYIH<QGLVQQDLKPVFWEITKL*KEIQLAKL

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	0.09 RPM	7.35 RPM
SRP007412_cerebellum	0.00 RPM	3.15 RPM
SRP007412_heart	0.00 RPM	6.03 RPM
SRP007412_kidney	0.08 RPM	26.65 RPM
SRP007412_liver	0.00 RPM	16.24 RPM
SRP007412_testis	0.00 RPM	23.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2518 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2518 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3716
Pongo abelii	retro_pabe_3140
Macaca mulatta	retro_mmul_1698

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000007376	1 retrocopy	retro_fcat_348,
Homo sapiens	ENSG00000167994	1 retrocopy	retro_hsap_3716,
Gorilla gorilla	ENSGGOG00000012399	1 retrocopy	retro_ggor_2513,
Macaca mulatta	ENSMMUG00000015148	1 retrocopy	retro_mmul_1698,
Nomascus leucogenys	ENSNLEG00000003273	1 retrocopy	retro_nleu_2858,
Pongo abelii	ENSPPYG00000003175	1 retrocopy	retro_pabe_3140,
Pan troglodytes	ENSPTRG00000003755	1 retrocopy	retro_ptro_2518 ,