RetrogeneDB ID: retro_pabe_3140

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:50810806..50811724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB3IL1
• Ensembl ID: ENSPPYG00000003175
• Aliases: None
• Description: RAB3A interacting protein (rabin3)-like 1 [Source:HGNC Symbol;Acc:9780]

Sequence

>retro_pabe_3140
TCCATAGGAATTCACAAGAAGGGCTCTGAGCTCCTGAAGGAGAAGCTGCACAAAGCTCACAAGGAGCTGCAGCTGAAGGA
CGAAGACTGTGAGCAGCTGTTCCTAGTGCAGGAGCAGCTGCACAGGAACTGGAGGAACTGTTGGCTAGCCTGTTTGAGGA
AGCCCACAAGATGGTGTGGGAAGCCAACATGCAGTAGGCAGTGTCAGAAAAGCAACTGAATGCGGAGGCATGGGGAAAGA
TAGGCATGGTGCAGGCAGAGGTGACAGCTTGAAGACACTGGTCATCATGTCCACACCAGCCTCTCCCAACTACAAGCTCC
ACCTGCACCTGCTGAGCCCCACTAAGAATGGGACCTGCAAGGCCCACTGCCAACATAAGAGCCCCAGCAGTGCCCTCTCC
TTGGCCTTGTGCCCCACTGTGAGACATGCCCTCACCTTGGACAAGGAGGTGGATGTGACACTATTGGCAGAGTTCCAAGC
CTGGAAGGAATTACCTACCCTGGACAAGACCTGTTCCTTGCTGCAAACGGTGTAGTGGGAGGATATGGAACCCTGCCTGG
ACTTCACAGTGCAGAATCTTTTGCCACAGGTGTAGGCCTCTGTGGGGGACACCACACTCACCATCAAGACTGTGGCTCTG
CAGAAGCTGCCTATAGTGAGGGTAACTGTGGTCAATTGTGGCAGTGCCAATATATGTGTCTTGAGCAATTTGGCCCATAC
CTGCCACCACCACCACATCTGGCTTTGTGACTTTGAGAGCCACTACCACATCTCACTGTCTTCTCAGGCCAGGATCACTG
CAGTGTGCAACTTTTTCATCTATATCTGCTACATCCACAAGGCCTGGTGCAACAGGATTTGAAGCCAGTGTTCTGGGAGA
TCACAAAGCTGTGAAAAGAGATACAGCTGGCCAAACTC

Alignment

ORF - retro_pabe_3140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.9 %
• Parental protein coverage: 80.58 %
• 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.LKDE.CE.L..V.EQL..QELEEL.ASLFEEAHKMV.EANM..A.S
Retrocopy SIGIHKKGSELLKEKLHKAHKELQLKDEDCEQLFLVQEQLH<QELEELLASLFEEAHKMVWEANMQ*AVS

Parental  EKQLK-EARGKIDMLQAEVTA-LKTLVITSTPASPNRELHPQLLSPTKAGPRKGHSRHKSTSSTLCPAVC
          EKQL..EA.GKI.M.QAEVTA.LKTLVI.STPASPN..LH..LLSPTK.G..K.H..HKS.SS.L..A.C
Retrocopy EKQLNAEAWGKIGMVQAEVTA<LKTLVIMSTPASPNYKLHLHLLSPTKNGTCKAHCQHKSPSSALSLALC

Parental  PAAGHTLTPDREGKEVDTVLFAEFQAWRS-PTLDKTCPFLERVYREDVGPCLDFTMQELSVLVRAAVEDN
          P...H.LT.D...KEVD..L.AEFQAW...PTLDKTC..L..V..ED..PCLDFT.Q.L...V.A.V.D.
Retrocopy PTVRHALTLD---KEVDVTLLAEFQAWKELPTLDKTCSLLQTV*WEDMEPCLDFTVQNLLPQV*ASVGDT

Parental  TLTIEPVASQTLPAVKVAEVDCSSTNTCALSGLTRTC-RHRIRLGDSKSHYYISPSSRARITAVCNFFTY
          TLTI..VA.Q.LP.V.V..V.C.S.N.C.LS.L..TC..H.I.L.D..SHY.IS.SS.ARITAVCNFF.Y
Retrocopy TLTIKTVALQKLPIVRVTVVNCGSANICVLSNLAHTCHHHHIWLCDFESHYHISLSSQARITAVCNFFIY

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	0.06 RPM	12.44 RPM
SRP007412_cerebellum	0.00 RPM	2.19 RPM
SRP007412_heart	0.00 RPM	4.03 RPM
SRP007412_kidney	0.03 RPM	57.34 RPM
SRP007412_liver	0.03 RPM	11.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3140 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3140 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3716
Pan troglodytes	retro_ptro_2518
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,