RetrogeneDB ID: retro_pabe_3723

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:11569975..11571014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIMK2
• Ensembl ID: ENSPPYG00000011730
• Aliases: None
• Description: LIM domain kinase 2 [Source:HGNC Symbol;Acc:6614]

Sequence

>retro_pabe_3723
GAATGCTTTGCCTGTATGAGCTGTAAGGTGACCATTGAGGATGGGGATGCATACGCCCCGGTGCTGCGTGTCACCCTATA
CTGTGGAAAGTGCCACAATGAGGTGGTGCTGGCACCCGTATTTGAGATACTCTCCACAGAGTCCATTCAGGACCAGCTGC
CCTACTCTGTCATGCTCATGTCCATGCTGGCCACCACAGAGGGCAGGCGGAGCTTCTCTGTGTCCATGGAGAATGCCTGC
TCCAACTATGTTACCACCGTGCAAGTAAAAGAGGTCAACCAGATGCACATCAGTCCCAACAGCTGCAATGCCATCCACCC
CAGGGACCGCATCCTGGAGATCAGTGGAACCCCCATCCACACACTCCAAGTAGAGGAGTTGGAGGATGCAATTAGCCAGA
TGAGCCAGACACTTCTGCTGTTGATTGAACATGACCCCGTCTCCCGGTGCCCAGCCCAGCTGCGGCTGGATGCCTGGCTC
TCTCCCCACATGCAGAATGCTGGACACCCTCATGCCCTCAGCACCCTGGACACCAAGGATAATCTGGAGGGGACGCTGAG
AAGATGCTCCCTAAGACTCAGTAACAGCATCTCCAAGTCCCCTAGCCCTAGCTCTCTAAAGGAGCCCCTGCTGCTCAGCC
ATGACGTCAGCTGCTGGGAATCCCTTTGTTGTTCCAGCACTTATTCAAAGCAGATCTTCCGGTCCTGTGACCTGATCCAC
GGGGAGGTCCTGGGGAAGGGCTTCTTTGGGCAGGCTATCAAAGTGACACACAAAGCCACAGGCAAAGTGATGGTCGTGAA
GGAATGAATGTGATGTGATGAGGAGAACCAGAAGACTTTTCTGACTGAAGTGAAAGTGACGTGAAGCCTGGACCACCCCC
ATGTGCTCAAGTTCATTGACGTGCTGTACAAGGACAAGAAGCTGAACTTGCTGAGAGGACATTGAGGGGGGCATGCTGAA
GGACCTTCTGCAAAGTGTGGACCCGTTCCCCTGGCAGCAGGAAGTCAGCTTGGCCAAAGGCATCGCCTCCAGAATGGCC

Alignment

ORF - retro_pabe_3723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.94 %
• Parental protein coverage: 59.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVLAPMFERLSTESVQEQLPYSVMLISMPATTEGRR
          ECFACMSCKV.IEDGDAYA.V...TLYCGKCHNEVVLAP.FE.LSTES.Q.QLPYSVML.SM.ATTEGRR
Retrocopy ECFACMSCKVTIEDGDAYAPVLRVTLYCGKCHNEVVLAPVFEILSTESIQDQLPYSVMLMSMLATTEGRR

Parental  GFSVSVESACSNYATTVQVKEVNRMHISPNNRNAIHPGDRILEINGTPVRTLRVEEVEDAISQTSQTLQL
          .FSVS.E.ACSNY.TTVQVKEVN.MHISPN..NAIHP.DRILEI.GTP..TL.VEE.EDAISQ.SQTL.L
Retrocopy SFSVSMENACSNYVTTVQVKEVNQMHISPNSCNAIHPRDRILEISGTPIHTLQVEELEDAISQMSQTLLL

Parental  LIEHDPVSQRLDQLRLEARLAPHIQNAGHPHALSTLDTKENLEGTLKRRSLRRSNSISKSPGPSSPKEPL
          LIEHDPVS....QLRL.A.L.PH.QNAGHPHALSTLDTK.NLEGTL.R.SLR.SNSISKSP.PSS.KEPL
Retrocopy LIEHDPVSRCPAQLRLDAWLSPHMQNAGHPHALSTLDTKDNLEGTLRRCSLRLSNSISKSPSPSSLKEPL

Parental  LFSRDISRSESLRCSSSYSQQIFRPCDLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKTF
          L.S.D.S..ESL.CSS.YS.QIFR.CDLIHGEVLGKGFFGQAIKVTHKATGKVMV.KE...CDEE.QKTF
Retrocopy LLSHDVSCWESLCCSSTYSKQIFRSCDLIHGEVLGKGFFGQAIKVTHKATGKVMVVKE*M*CDEENQKTF

Parental  LTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEY-IEGGTLKDFLR-SMDPFPWQQKVRFAKGIASGMA
          LTEVKV..SLDHP.VLKFI.VLYKDKKLNLL......G.....F...S.DPFPWQQ.V..AKGIAS.MA
Retrocopy LTEVKVT*SLDHPHVLKFIDVLYKDKKLNLLRGH<LRGAC*RTFCK<SVDPFPWQQEVSLAKGIASRMA

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	12.72 RPM
SRP007412_cerebellum	0.00 RPM	14.96 RPM
SRP007412_heart	0.00 RPM	2.83 RPM
SRP007412_kidney	0.07 RPM	12.60 RPM
SRP007412_liver	0.00 RPM	14.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3723 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3723 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4783
Pan troglodytes	retro_ptro_3184
Gorilla gorilla	retro_ggor_2978

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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,