RetrogeneDB ID: retro_nleu_2858

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397454.1:477954..478870(+)
• Located in intron of: ENSNLEG00000015425

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB3IL1
• Ensembl ID: ENSNLEG00000003273
• Aliases: None
• Description: None

Sequence

>retro_nleu_2858
TCCATAGGAATTCACAAGAAGGGCTCTGAGCTCCTGAAGGAGAAGCTGCACAAAGCTCACAAGGAGCTGCAGCTGAAGGA
TGAAGACTGTGAGCAGCTGTTCCTAGTGCAGGAGCAGCCGCACAGGAGCTTGGAGCTGATGGCCAGCCAGTTTGAGGAAG
CCCACAAGATGGTGTGGGAAGCCAACATACAGTAGGCAGTGTCAGAAAAGCAGCTGAATGTGGAGGCATGGGGAAAGATA
GGCATGCTGCAGGCAGAGGTGACAGCTTGAAGACACTGGTCATCATGTCCACACCAGCCTCTCCCAACTAGAAGCTCCAC
CTGCACCTGCTGAGCCCCACTAAGGATGGGCCCTGCAAGGCCCACTGTCAACATAAGAGCATCAGCAGTGCCCTCTCCTT
GGCCTTGTGCCCCACTGTGAGACATGCCCTCACCTTGGACAAGGAGGTGGATGTGACATTATTGGCAGAGTTCCAAGTCT
GGAAGGAATTACCTACCCTGGACAAGACCTGTTCCTTGCTGCAAAGGGTCTAGTGGGAGGATATGGATCCCTGCCTGGAC
TTCACAGTGCAGAATCTCTTGCCACAGGTGTAGGCCTCTGTGGGGGACAACACACTCACCATCAAGACTGTGGCTTTGCA
GAAGCTGCCTGTAGTGAGGGTAACTGTGGTCAATTGTGGCAGTGCCAATAGATGTGTCTTGAGCAATTTGGCCTATACCT
GCCACCACCACCACATCTGGCTTTGTGACTTTGAGAGCCACTACCACATCTCACTGTCTTCTCAGGCTAGGATCACTGTA
GTGTGCAACTTTTTCATCTATATCTGCTACATCCACAAGGCCTGCTGCAACAGGATTTGAAGCCGGTGTTCTGGGAGATC
ACAAAGCTGTGAAAAGAGATACAGCTGGCCAAATTG

Alignment

ORF - retro_nleu_2858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.82 %
• Parental protein coverage: 80.63 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMEIREKGSEFLKEELHRAQKELKLKDEECERLSKVREQLEQELEELTASLFEEAHKMVREANMKQAASE
          S..I..KGSE.LKE.LH.A.KEL.LKDE.CE.L..V.EQ....LE.L.AS.FEEAHKMV.EAN...A.SE
Retrocopy SIGIHKKGSELLKEKLHKAHKELQLKDEDCEQLFLVQEQPHRSLE-LMASQFEEAHKMVWEANIQ*AVSE

Parental  KQLR-EARGKIDMLQAEVTA-LKTLVITSTPASPNRELHPQLLSPTKAGPRKGHSRHKSTSSTLCPAVCP
          KQL..EA.GKI.MLQAEVTA.LKTLVI.STPASPN..LH..LLSPTK.GP.K.H..HKS.SS.L..A.CP
Retrocopy KQLNVEAWGKIGMLQAEVTA<LKTLVIMSTPASPN*KLHLHLLSPTKDGPCKAHCQHKSISSALSLALCP

Parental  AAGHTLTPDREGKEVDTILFAEFQAWRESPTLDKTCPFLERVYREDVGPCLDFTMQELSALVRAAVEDNT
          ...H.LT.D...KEVD..L.AEFQ.W.E.PTLDKTC..L.RV..ED..PCLDFT.Q.L...V.A.V.DNT
Retrocopy TVRHALTLD---KEVDVTLLAEFQVWKELPTLDKTCSLLQRV*WEDMDPCLDFTVQNLLPQV*ASVGDNT

Parental  LTIEPVASQTLPAVKVAEVDCSSTNTCALSGLTRTC-RHRIRLGDSKSHYYISPSSRARITAVCNFFTYI
          LTI..VA.Q.LP.V.V..V.C.S.N.C.LS.L..TC..H.I.L.D..SHY.IS.SS.ARIT.VCNFF.YI
Retrocopy LTIKTVALQKLPVVRVTVVNCGSANRCVLSNLAYTCHHHHIWLCDFESHYHISLSSQARITVVCNFFIYI

Parental  RYIQ-QGLVRQDAEPMFWEIMRLRKEMSLAKL
          .YI..QGL..QD..P.FWEI..L.KE..LAKL
Retrocopy CYIH<QGLLQQDLKPVFWEITKL*KEIQLAKL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2858 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,