RetrogeneDB ID: retro_ptro_3184

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:11632300..11633358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIMK2
• Ensembl ID: ENSPTRG00000014266
• Aliases: None
• Description: LIM domain kinase 2 [Source:HGNC Symbol;Acc:6614]

Sequence

>retro_ptro_3184
GAGTTCAAGTACCATCCAGAATGCTTTGCCTGTATGAGCTATAAGGTGACCATTGAGGATGGGGATGCATACGCCCTGGT
GCTGCGTGTCACCCTATACTGTGGAAAGTGCCACAAATGAGGTGATGCTGGCATCCATATTTGAGATACTCTCCACAGAG
TCCATTCAGGACCAGCTGCCCTACTCTGTCATGCTCATGTCCATGCTGGCCATCACAGAGGGCAGGCGGAGCTTCTCTGT
GTCCGTGGAGAATGCCTGCTCCAACTATGTTACCACCGTGTCAGTAAAAGAGGTCAACCAGATGCACATCAGTCCCAACA
GCCGCAATGCCATCCACCCCAGGGACCACATCCTGGAGATCAGTGGAACCCCCACCCACACACTCCAAGTAGAGGAGTTG
GAGGATGCAATTAGCCAGATGAGCCAGACACTTCTGCTGTTGATTGAACATGACCCTGTCTCCCGGTCCCCAGCCCAGCT
GCGGCTGGATGCCTGGCTCTCTCCCCACACGCAGAATGCTGGACACCCTCATGCCCTCAGCACCCTGGACACCAAGGATA
ATCTGGAGGGGACGCTGAGAAGATGCTCCCTAAGACTCAGTAACAGCATCTCCAAGTCCCCTAGCCCTAGCTCTCCAAAG
GAGCCCCTGCTGCTCAGCCGTGACATCAGCTGCTGGGAATCCCTTTGTTGTTCCAGCACTTACTCAAAGCAGAACTTCCG
GTCCTGTGACCTGATCCACGGGGAGGTCCTGGGGAAGGGTTTCTTTGGGCAGGCTATCAAAGTGACACACAAAGCCACAG
GCAAAGTGTTGGTCATGAAGAAATTAATGTGATGTGATGAGGAGAACCAGGAGACTTTTCTGACTGAAGTGAAAGTGACG
TGAAGCCTGGACCACCCCAATGTGCTCAAGTTCATTGGCGTGCTGTACAAGGACAAGAAGCTGAACCTGCTGAGAGGACA
TTGAGGGGGGCATGCTGAAGGACCTTCTGCAAAGTGTGGACCCGTTCCCCTGGCAGCAGGAAGTCAGCTTGGCCAAAGGC
ATTGCCTCCAGAATGGCC

Alignment

ORF - retro_ptro_3184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.09 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCH-NEVVLAPMFERLSTESVQEQLPYSVTLISMP
          EFKYHPECFACMS.KV.IEDGDAYALV...TLYCGKCH.NEV.LA..FE.LSTES.Q.QLPYSV.L.SM.
Retrocopy EFKYHPECFACMSYKVTIEDGDAYALVLRVTLYCGKCH>NEVMLASIFEILSTESIQDQLPYSVMLMSML

Parental  ATTEGRRGFSVSVESACSNYATTVQVKEVNRMHISPNNRNAIHPGDRILEINGTPVRTLRVEEVEDAISQ
          A.TEGRR.FSVSVE.ACSNY.TTV.VKEVN.MHISPN.RNAIHP.D.ILEI.GTP..TL.VEE.EDAISQ
Retrocopy AITEGRRSFSVSVENACSNYVTTVSVKEVNQMHISPNSRNAIHPRDHILEISGTPTHTLQVEELEDAISQ

Parental  TSQTLQLLIEHDPVSQRLDQLRLEARLAPHMQNAGHPHALSTLDTKENLEGTLRRRSLRRSNSISKSPGP
          .SQTL.LLIEHDPVS....QLRL.A.L.PH.QNAGHPHALSTLDTK.NLEGTLRR.SLR.SNSISKSP.P
Retrocopy MSQTLLLLIEHDPVSRSPAQLRLDAWLSPHTQNAGHPHALSTLDTKDNLEGTLRRCSLRLSNSISKSPSP

Parental  SSPKEPLLFSRDISRSESLRCSSSYSQQIFRPCDLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCD
          SSPKEPLL.SRDIS..ESL.CSS.YS.Q.FR.CDLIHGEVLGKGFFGQAIKVTHKATGKV.VMK.L..CD
Retrocopy SSPKEPLLLSRDISCWESLCCSSTYSKQNFRSCDLIHGEVLGKGFFGQAIKVTHKATGKVLVMKKLM*CD

Parental  EETQKTFLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEY-IEGGTLKDFLR-SMDPFPWQQKVRFAKG
          EE.Q.TFLTEVKV..SLDHPNVLKFIGVLYKDKKLNLL......G.....F...S.DPFPWQQ.V..AKG
Retrocopy EENQETFLTEVKVT*SLDHPNVLKFIGVLYKDKKLNLLRGH<LRGAC*RTFCK<SVDPFPWQQEVSLAKG

Parental  IASGMA
          IAS.MA
Retrocopy IASRMA

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	9.38 RPM
SRP007412_cerebellum	0.00 RPM	20.94 RPM
SRP007412_heart	0.00 RPM	5.10 RPM
SRP007412_kidney	0.00 RPM	30.70 RPM
SRP007412_liver	0.00 RPM	46.16 RPM
SRP007412_testis	0.00 RPM	23.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3184 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3184 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4783
Gorilla gorilla	retro_ggor_2978
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 ,