RetrogeneDB ID: retro_nleu_1230

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:12849810..12851960(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKN2
• Ensembl ID: ENSNLEG00000010197
• Aliases: None
• Description: None

Sequence

>retro_nleu_1230
CAGAAGTTGGACCTTTTAAAGTATTCATTAGAGCAAAGATTAAATGAACTCCCCAAGAATCATCCCAAAAGCAGTATTAT
TACTGAAGAACTTTCACTTGTTGCCGCATCACCAACACTAAGTCCACGTCAAAGTATGATATCTACACAAAATCAATATA
GTACACCATCCAAACCAGCAGCATTAACAGGGACTTTGGAAGTTGGTCTCATGGGCTGCCAAGATATCCTAGAGAATGTC
CCTGGACGGTCAAAAGCAACATCAATTGCACTGCCTGGTTGGAGTTCAAGTGAAACCAGATCATCTTTCATGAGCAGAAC
GAGTAAAAGTAAAAGTGGAAGTAGTCGAAATCTTCTAAAAACCGATGACTTGTCCAATGATGTCTGTGCTGTTTTGAAGC
TCGATAATACTGTGGTTGGCCAATCTAGCTGGAAAGCCATTTCCAATCAGTCATGGGACCAGAAGTTTACACTGGAACTG
GACAGGTCACGTGAACTGGAAATTTCAGTTTATTGGCGTGATTGGCGGTCTCTGTGTGCTGTAAGATTTCTGAGGTTAGA
AGATTTTTTAGACAACCAACGGCATGGCATGTGTCTCTATTTGGAACCACAGGGTACTTTATTTGCAGAGGTTACCTTTT
TAAATCCAGTTATTGAAAGAAGACCAAAACTTCAAAGACAAAAGAAAATTTTTTCAAAGCAACAAGGCAAAACATTTCTC
AGAGCTCCTCAAATGAATATTAATATTGCCACTTGGGGAAGGCTAGTAAGAAGAGCTATTCATACAGTAAATCATTCTGG
CACCTTCAGCCCTCAAGCTCCTGTGCCTACTACAGTGCCAGTGGTTGATGTACGCATCCCTGAACTAGCACCTCCAGCTA
GTGATTCTACAGTAACCAAATTGGACTTTGATCTTGAGCCTGAACCTCCTCCAGCCCCACCACGAGCTTCTTCCCTTGGA
GAAATAGATGAATCTTCTGAATTAAGAGTTTTGGATACACCAGGACAGGATTCAGAGACTGCTTTTGATATTGAGAATGA
CAGACATAGTATACTTCCAAAATCTCAATCTGAATACAAGCCTGATACTCCTCAGTCAGGCCTAGAATATAGTGGTATTC
AAGAACTTGAGGACAGAAGATCTCAGCAAAGGTTTCAGTTTAATCTACAAGATTTCAGGTGTTGTGCTGTCTTGGGAAGA
GGAAATTTTGGAAAGTGCTTTTAGCTGAATATAAACACACAAATGAGATGTTTGCTATAAAATCCTTAAAGAAAGGAGAT
ATTGTGGCTCAAGATGAAGTAGACAGACTGATGTCTGAAAAAAGAATTTTTGAAACTGTGAATAGTGTAAGGCATCCCTT
TTTGGTGAACCTTTTTGCATGTTTCCAAACCAAAGAGCATGTTTGCTTTGTAATGGAATATGCTGCCGTTGGGGACCTAA
TGATGCACATTCATACTGACGTCTTTTCTGAACCAAGAGCTGTATTTTATGCTGCTTGTGTAGTTCTTGGGTTGCAGTAT
TTACATGAACACAAAATTGTTTATAGAGATTTGAAATTGGGTAACTTATTGCTAGATACAAAGGGCTGTGTGAAAATTGC
TGATTTTGGTGTTTGCAGAGAAGGAATGGAATATGGAGATAGAACAAGCACATTTTGTGGCACTCCTGAATTTCTTGCCC
CAGAAGTATTAACAGAAACTTCTTATACAAGGGCTGTAGATTGGTGGGGCCTTGGCGTGCTTATATATGTAATGCTTGTT
GGTAAGTCTCCCTTTCATGGTTATGATAAAGAGGAAGTTTTTGACAGTATTATAAATGATGAAGTAAGGTATCCAAGGTT
CTTATCTGCAGAAGCCATTTCTATAATGAGAAGGCTGTTAAGAAGAAATCCTGAGCGGCGCCTTGGGGCTAGCGAGAAAG
ATACAGAGGATGTAAAAAAGCACCCATTTTTCCAGCTAATTGATTGGAGCGCTCTGATGGACAAAAAAGTAAAGCCACCA
TTTATACATACCATAAGATGAGAAGATGTTAGTAATTTTGATGATGAATTTACCTCAGAAGCACCTATTCTGACTCCACC
CCTAGAACCAAGGATACTTTCGGAAGAGGAGCAGGAAATGTTCAGAAATTTTGACTACATTGCTGATTGG

Alignment

ORF - retro_nleu_1230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.52 %
• Parental protein coverage: 72.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKLDLLKYSLEQRLNELPKNHPKSSIIIEELSLVAASPTLSPRQSMISTQNQYSTLSKPAALTGILEVRL
          QKLDLLKYSLEQRLNELPKNHPKSSII.EELSLVAASPTLSPRQSMISTQNQYST.SKPAALTG.LEV.L
Retrocopy QKLDLLKYSLEQRLNELPKNHPKSSIITEELSLVAASPTLSPRQSMISTQNQYSTPSKPAALTGTLEVGL

Parental  MGCQDILENVPGRSKATSVALPGWSPSETRSSFMSRTSKSKSGSSRNLLKTDDLSNDVCAVLKLDNTVVG
          MGCQDILENVPGRSKATS.ALPGWS.SETRSSFMSRTSKSKSGSSRNLLKTDDLSNDVCAVLKLDNTVVG
Retrocopy MGCQDILENVPGRSKATSIALPGWSSSETRSSFMSRTSKSKSGSSRNLLKTDDLSNDVCAVLKLDNTVVG

Parental  QTSWKPISNQSWDQKFTLELDRSRELEISVYWRDWRSLCAVKFLRLEDFLDNQRHGMCLYLEPQGTLFAE
          Q.SWK.ISNQSWDQKFTLELDRSRELEISVYWRDWRSLCAV.FLRLEDFLDNQRHGMCLYLEPQGTLFAE
Retrocopy QSSWKAISNQSWDQKFTLELDRSRELEISVYWRDWRSLCAVRFLRLEDFLDNQRHGMCLYLEPQGTLFAE

Parental  VTFFNPVIERRPKLQRQKKIFSKQQGKTFLRAPQMNINIATWGRLVRRAIPTVNHSGTFSPQAPVPTTVP
          VTF.NPVIERRPKLQRQKKIFSKQQGKTFLRAPQMNINIATWGRLVRRAI.TVNHSGTFSPQAPVPTTVP
Retrocopy VTFLNPVIERRPKLQRQKKIFSKQQGKTFLRAPQMNINIATWGRLVRRAIHTVNHSGTFSPQAPVPTTVP

Parental  VVDVRIPELAPPASDSTVTKLDFDLEPEPPPAPPRVSSLGEIDESSELRLLDAHDGDSETAFDIENDRNS
          VVDVRIPELAPPASDSTVTKLDFDLEPEPPPAPPR.SSLGEIDESSELR.LD....DSETAFDIENDR.S
Retrocopy VVDVRIPELAPPASDSTVTKLDFDLEPEPPPAPPRASSLGEIDESSELRVLDTPGQDSETAFDIENDRHS

Parental  ILPKSQSEYKPDTPQSGLEYSGIQELEDRSSQQRFQFNLQDFRCCAVLGRGHFG-KVLLAEYKHTNEMFA
          ILPKSQSEYKPDTPQSGLEYSGIQELEDR.SQQRFQFNLQDFRCCAVLGRG.FG.KVLLAEYKHTNEMFA
Retrocopy ILPKSQSEYKPDTPQSGLEYSGIQELEDRRSQQRFQFNLQDFRCCAVLGRGNFG<KVLLAEYKHTNEMFA

Parental  IKALKKGDIVARDEVDSLMCEKRIFETVNSVRHPFLVNLFACFQTKEHVCFVMEYAAGGDLMMHIHTDVF
          IK.LKKGDIVA.DEVD.LM.EKRIFETVNSVRHPFLVNLFACFQTKEHVCFVMEYAA.GDLMMHIHTDVF
Retrocopy IKSLKKGDIVAQDEVDRLMSEKRIFETVNSVRHPFLVNLFACFQTKEHVCFVMEYAAVGDLMMHIHTDVF

Parental  SEPRAVFYAACVVLGLQYLHEHKIAHRDLKLENLLLDTEGFVKIADFGLCKEGMGYRDRTSTFCGTPLYL
          SEPRAVFYAACVVLGLQYLHEHKI..RDLKL.NLLLDT.G.VKIADFG.C.EGM.Y.DRTSTFCGTP..L
Retrocopy SEPRAVFYAACVVLGLQYLHEHKIVYRDLKLGNLLLDTKGCVKIADFGVCREGMEYGDRTSTFCGTPEFL

Parental  APEVITEISYTRAVDWWGLGVLIYQMLVGDYPFRGGDEEKLFDSIVNDEVRYPRFLSTEAISIMRRLLRR
          APEV.TE.SYTRAVDWWGLGVLIY.MLVG..PF.G.D.E..FDSI.NDEVRYPRFLS.EAISIMRRLLRR
Retrocopy APEVLTETSYTRAVDWWGLGVLIYVMLVGKSPFHGYDKEEVFDSIINDEVRYPRFLSAEAISIMRRLLRR

Parental  NPKRRLGASKKDAEDVKKHPFFRLIDWSALMDKKVKPPFIPTIRGREDVSHFDDEFTSEAPILTPPRERR
          NP.RRLGAS.KD.EDVKKHPFF.LIDWSALMDKKVKPPFI.TIR..EDVS.FDDEFTSEAPILTPP.E.R
Retrocopy NPERRLGASEKDTEDVKKHPFFQLIDWSALMDKKVKPPFIHTIR-*EDVSNFDDEFTSEAPILTPPLEPR

Parental  ILSEEEQEMFRDFDYTADW
          ILSEEEQEMFR.FDY.ADW
Retrocopy ILSEEEQEMFRNFDYIADW

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_1230 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000010197	4 retrocopies	retro_nleu_1230 , retro_nleu_2252, retro_nleu_2861, retro_nleu_3074,