RetrogeneDB ID: retro_ggor_2978

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:11580911..11581948(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIMK2
• Ensembl ID: ENSGGOG00000003489
• Aliases: None
• Description: None

Sequence

>retro_ggor_2978
GAATGCTTTGCCTGTATGAGCTATAAGGTGACCATTGAGGATGGGGATGCATACGCCCTGGTGCTGCGTGTCACCCTATA
CTGTGGAAAGTGCAACAAATGAGGTGGTGCTGGCACCCATATTTGAGATACTCTCCACAGAGTCCATTCAGGACCAGCTG
CCCTACTCTGTCATGCTCATGTCCATGCTGGCCATCACAGAGGGCAGGCGGAGCTTCTCCGTGTCCGTGGAGAATGCCTG
CTCCAACTATGTTACCACCGTGCAAGTAAAAGAGGTCAACCAGATGCACATCAGTCCCAACAGCCGCAATACCATCCACC
CCAGGGACCACATCCTGGAGATCAGTGGAACCCCCACCCACACACTCCAAGTAAAGGAGTTGGAGGATGCAATTAGCCAG
ATGAGCCAGACACTTCTGCTGTTGATTGAACATGACCCCATCTCCCGGTCCCCAGCCCAGCTGCGGCTGGATGCCTGGCT
CTCTCCCCACACGCAGAATGCTGGACACCCTCACGCCCTCAGCACCCTGGACACCAAGAATAATCTGGAGGGGACGCTGA
GAAGATGCTCCCTAAGACTCAGTAACAGCATCTCCAAGTCCCCTAGCCCTAGCTCTCCAAAGGAGCCCCTGCTGCTCAGC
CGTGACATCAGCTGCTGGGAATCCCTTTGTTGTTCCAGCACTTACTCAAAGCAGATCTTCCGGTCCTGTGACCTGATCCA
CGGGGAGGTCCTGGGGAAGGGCTTCTTTGGGCAGGCTATCAAAGTGACACACAAAGCCACAGGCAAAGTGTTGGTCATGA
AGGAATTAGTGCGATGTGATGAGGAGAACCAGAAGACTTTTCTGACTGAAGTGAAAGTGACGTGAAGCCTGGACCACCCC
AATGTGCTCAAGTTCATTGGCGTGCTGTACAAGGACAAGAAGCTGAACCTGCTGAGAGGACATTGAGGGGGGCATGCTGA
AGGACCTTCTGCAAAGTGTGGACCCGTTCCCCTGGCAGCAGGAAGTCAGCTTGGCCAAAGGCATTGCCTCCAGAATG

Alignment

ORF - retro_ggor_2978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 55.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ECFACMSCKVIIEDGDAYALVQHATLYCGKCH-NEVVLAPMFERLSTESVQEQLPYSVTLISMPATTEGR
          ECFACMS.KV.IEDGDAYALV...TLYCGKC..NEVVLAP.FE.LSTES.Q.QLPYSV.L.SM.A.TEGR
Retrocopy ECFACMSYKVTIEDGDAYALVLRVTLYCGKCN>NEVVLAPIFEILSTESIQDQLPYSVMLMSMLAITEGR

Parental  RGFSVSVESACSNYATTVQVKEVNRMHISPNNRNAIHPGDRILEINGTPVRTLRVEEVEDAISQTSQTLQ
          R.FSVSVE.ACSNY.TTVQVKEVN.MHISPN.RN.IHP.D.ILEI.GTP..TL.V.E.EDAISQ.SQTL.
Retrocopy RSFSVSVENACSNYVTTVQVKEVNQMHISPNSRNTIHPRDHILEISGTPTHTLQVKELEDAISQMSQTLL

Parental  LLIEHDPVSQRLDQLRLEARLAPHMQNAGHPHALSTLDTKENLEGTLRRRSLRRSNSISKSPGPSSPKEP
          LLIEHDP.S....QLRL.A.L.PH.QNAGHPHALSTLDTK.NLEGTLRR.SLR.SNSISKSP.PSSPKEP
Retrocopy LLIEHDPISRSPAQLRLDAWLSPHTQNAGHPHALSTLDTKNNLEGTLRRCSLRLSNSISKSPSPSSPKEP

Parental  LLFSRDISRSESLRCSSSYSQQIFRPCDLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKT
          LL.SRDIS..ESL.CSS.YS.QIFR.CDLIHGEVLGKGFFGQAIKVTHKATGKV.VMKEL.RCDEE.QKT
Retrocopy LLLSRDISCWESLCCSSTYSKQIFRSCDLIHGEVLGKGFFGQAIKVTHKATGKVLVMKELVRCDEENQKT

Parental  FLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEY-IEGGTLKDFLR-SMDPFPWQQKVRFAKGIASGM
          FLTEVKV..SLDHPNVLKFIGVLYKDKKLNLL......G.....F...S.DPFPWQQ.V..AKGIAS.M
Retrocopy FLTEVKVT*SLDHPNVLKFIGVLYKDKKLNLLRGH<LRGAC*RTFCK<SVDPFPWQQEVSLAKGIASRM

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	10.02 RPM
SRP007412_cerebellum	0.00 RPM	13.87 RPM
SRP007412_heart	0.00 RPM	5.47 RPM
SRP007412_kidney	0.00 RPM	14.68 RPM
SRP007412_liver	0.00 RPM	8.99 RPM
SRP007412_testis	0.00 RPM	21.86 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_2978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2978 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4783
Pan troglodytes	retro_ptro_3184
Pongo abelii	retro_pabe_3723

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000182541	1 retrocopy	retro_hsap_4783,
Gorilla gorilla	ENSGGOG00000003489	1 retrocopy	retro_ggor_2978 ,
Pongo abelii	ENSPPYG00000011730	1 retrocopy	retro_pabe_3723,
Pan troglodytes	ENSPTRG00000014266	1 retrocopy	retro_ptro_3184,