RetrogeneDB ID: retro_ggor_2513

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:33928352..33929180(+)
• Located in intron of: ENSGGOG00000008112

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB3IL1
• Ensembl ID: ENSGGOG00000012399
• Aliases: None
• Description: None

Sequence

>retro_ggor_2513
GAGCAGCTGGTCCTAGTGCAGGAGCAGCTGCACAGGAGCTGGAGGAGCTGATGACTGGCCTATTTGAGGAAGCCCACAAG
ATGGTGTGGGAAGCCAGCGTACAGTAGGCAGTGTCAGAAAAGCAGCTGAATGCAGAGGCATGGGGAAAGATAGGCATGCT
GCAGGCAGAGGTGACAGCTTGAAGACACTGGTCATCATGTCCACACCAGCCTCTCCCAACTACAAGCTCCACCTGCACCT
GCTGAGCCCCACTAAGGGTGGGCCCTGCAAGGCCCACTGCCAACCTAAGAGCACCAGCAGTGCCCTCTCCTTGACCTTGT
GCCCCACTGTGAGACATGCCCTCACCTTGGACAAGGAGGTGGATGTGACACTATTGGCAGAGTTCCAAGCCTGGAAGGAA
TTACCTACCTTGGACAAGACCTGTTCCTTGCTGCAAAGGGTGTAGTGGGAGGATATGGACCCCTGCCTGGACTTCACAGT
GCAGAATCTCTTGCCACAGGTGTAGGCCTCTATGGGGGACACCACACTCACCATCAAGACTGTGGCTCTGCAGAAGCTGC
CTATAGTGAGGGTAACTGTGGTCAATTGTGTCAGTGCCAATATATGTGTCTTGAGCAATTTGGCCCATACCTGCCACCAC
CACCACATCTGGCTTTGTGACTTTGCGAGCCACTACCACATCTCACTGTCTTCTCAGGCCAGGATCACTGCAGTGTGCAA
CTTTTTCATCTATATCTGCTACATCCACAAGGCCTGGTGCAACAGGATTTGAAGCCAGTGTTCTGGGAGATCACAAAGCT
GTGAAAAGAGATACAGCTGGCCAAACTC

Alignment

ORF - retro_ggor_2513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.9 %
• Parental protein coverage: 72.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ERLSKVREQLE-QELEELTASLFEEAHKMVREANMKQAASEKQLK-EARGKIDMLQAEVTA-LKTLVITS
          E.L..V.EQL..QELEEL...LFEEAHKMV.EA....A.SEKQL..EA.GKI.MLQAEVTA.LKTLVI.S
Retrocopy EQLVLVQEQLH<QELEELMTGLFEEAHKMVWEASVQ*AVSEKQLNAEAWGKIGMLQAEVTA<LKTLVIMS

Parental  TPASPNRELHPQLLSPTKAGPRKGHSRHKSTSSTLCPAVCPAAGHTLTPDREGKEVDTILFAEFQAWRES
          TPASPN..LH..LLSPTK.GP.K.H...KSTSS.L....CP...H.LT.D...KEVD..L.AEFQAW.E.
Retrocopy TPASPNYKLHLHLLSPTKGGPCKAHCQPKSTSSALSLTLCPTVRHALTLD---KEVDVTLLAEFQAWKEL

Parental  PTLDKTCPFLERVYREDVGPCLDFTMQELSVLVRAAVEDNTLTIEPVASQTLPTVKVAEVDCSSTNTCAL
          PTLDKTC..L.RV..ED..PCLDFT.Q.L...V.A...D.TLTI..VA.Q.LP.V.V..V.C.S.N.C.L
Retrocopy PTLDKTCSLLQRV*WEDMDPCLDFTVQNLLPQV*ASMGDTTLTIKTVALQKLPIVRVTVVNCVSANICVL

Parental  SGLTRTC-RHRIRLGDSKSHYYISPSSRARITAVCNFFTYIRYIQ-QGLVRQDAEPMFWEIMRLRKEMSL
          S.L..TC..H.I.L.D..SHY.IS.SS.ARITAVCNFF.YI.YI..QGLV.QD..P.FWEI..L.KE..L
Retrocopy SNLAHTCHHHHIWLCDFASHYHISLSSQARITAVCNFFIYICYIH<QGLVQQDLKPVFWEITKL*KEIQL

Parental  AKL
          AKL
Retrocopy AKL

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	0.14 RPM	7.19 RPM
SRP007412_cerebellum	0.04 RPM	2.21 RPM
SRP007412_heart	0.06 RPM	4.75 RPM
SRP007412_kidney	0.20 RPM	15.25 RPM
SRP007412_liver	0.24 RPM	4.93 RPM
SRP007412_testis	0.21 RPM	42.48 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2513 has 0 orthologous retrocopies within eutheria group .

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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,