RetrogeneDB ID: retro_nleu_1360

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397290.1:21974721..21975935(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN11
• Ensembl ID: ENSNLEG00000000078
• Aliases: None
• Description: None

Sequence

>retro_nleu_1360
AAGGAACTGAAATACAACGTTGGTGGAGGAGAACGGTTTGATTCTTTGACAGATCTTGAGGAACATTACAAGAAGAATCC
TATGGTGGAAACACTGGTTACACTACTACAACTCAAGCAGCCCCTTAACACGACTCGTATAAATGCTGCTGAAATAGAAA
GCAGAGTTCGAGAACTAAGCAAATTAGCTGAGACAACAGATAAAGTCAAACAAGGCTTTTGGGAAAAATTTGAGACACTA
CAACAACAAGAGTGCAAACTTCTCTACAGCTGAAAAGAAGGTCAAAGGCAAGAAAACAGAAACAAAAATAGATATAAAAA
CATCCTGCCCTTTGATCATACCACAGTTGTCCTACACGACAGTGAGCCCAGTGAGCCTGTTTCAGATTACATCAAAGCAG
ATATCATCATTCCTGAATTTGACACCAAGTGCCACAATTCAAAGCCCTAAAAGAGTTACATTGCCACACAAGACTGCCTG
CAAAACACGGTGAATGACTTTTGGCGGATGGTATTCCAGGAAAACTCCCTAGTGATTGTCATGACAACAAAAGAAGTGTA
GAGAGGAAAGAGTAAATGTGTCAAATACTGGCCTGATGAGTATGCTCTAAAAGAATACGGCGTCATGCATGTTAGGAACG
TCAGAGATAGCGCCTCTCATGACTATACGCTAAGAGAACTTAAACTTTCAAAGGTTGGACGAGGGAACATGGAGAGAAGG
GTCTGGCAATACCACTTTCGGACTTGGCCGGACCATGGAGTGCCCAGTGACCCGGGGGCATGCTGGACTTCCTGGAGGAG
GTGTACCATAAGCAGGAGAGCATCATGGATGCAGGGCCAGTCGTGGTGCACTGCAGTGCTGGAATTGGCCAGACAGGGAC
ATTCATTGTGATTGATATTCTTATTGACATCGTCAGAGAGAAAGGTGTTGACTGCAACATTGATGTTCCCAAAACCATCC
AGATGGTGCAGTCTCAGAGGTCAGGGATGGTCCAGACAGAAGCATAGTACCGATTTATCTATATGACAGTCCAGCATTAT
ATTGAAACACTGCAGCTCAGGATTGAAGAAGAGCAGAAAAGCAAGAGGAAAGGGCACGAATATACAGATATTAAATATTC
TCTAGCAGACCAGACAAGTGGAGATCAGAGCCCCCTCTTGCCTTGTACTCCAACGCCACCGTGTGCAGAAATGAGAGAAG
ACAGTGCTAGAGTC

Alignment

ORF - retro_nleu_1360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.27 %
• Parental protein coverage: 79.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVK
          .ELKY.VGGGERFDSLTDL.EHYKKNPMVETL.T.LQLKQPLNTTRINAAEIESRVRELSKLAETTDKVK
Retrocopy KELKYNVGGGERFDSLTDLEEHYKKNPMVETLVTLLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVK

Parental  QGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEF
          QGFWE.FETLQQQECKLLYS.KEGQRQEN.NKNRYKNILPFDHT.VVLHD..P.EPVSDYI.A.II.PEF
Retrocopy QGFWEKFETLQQQECKLLYS*KEGQRQENRNKNRYKNILPFDHTTVVLHDSEPSEPVSDYIKADIIIPEF

Parental  ETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMR
          .TKC.NSKP.KSYIATQ.CLQNTVNDFWRMVFQENS.VIVMTTKEV.RGKSKCVKYWPDEYALKEYGVM.
Retrocopy DTKCHNSKP*KSYIATQDCLQNTVNDFWRMVFQENSLVIVMTTKEV*RGKSKCVKYWPDEYALKEYGVMH

Parental  VRNVKESAAHDYTLRELKLSKVGQALLQGNTERTVWQYHFRTWPDHGVPSD-PGGVLDFLEEVHHKQESI
          VRNV..SA.HDYTLRELKLSKVG.....GN.ER.VWQYHFRTWPDHGVPSD.PGG.LDFLEEV.HKQESI
Retrocopy VRNVRDSASHDYTLRELKLSKVG----RGNMERRVWQYHFRTWPDHGVPSD<PGGMLDFLEEVYHKQESI

Parental  MDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQ
          MDAGPVVVHCSAGIG.TGTFIVIDILIDI.REKGVDC.IDVPKTIQMV.SQRSGMVQTEA.YRFIYM.VQ
Retrocopy MDAGPVVVHCSAGIGQTGTFIVIDILIDIVREKGVDCNIDVPKTIQMVQSQRSGMVQTEA*YRFIYMTVQ

Parental  HYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARV
          HYIETLQ.RIEEEQKSKRKGHEYT.IKYSLADQTSGDQSPL.PCTPTPPCAEMREDSARV
Retrocopy HYIETLQLRIEEEQKSKRKGHEYTDIKYSLADQTSGDQSPLLPCTPTPPCAEMREDSARV

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_1360 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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051,
Homo sapiens	ENSG00000179295	5 retrocopies	retro_hsap_2823, retro_hsap_3061, retro_hsap_3302, retro_hsap_3670, retro_hsap_4062,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962,
Macaca mulatta	ENSMMUG00000013253	4 retrocopies	retro_mmul_1501, retro_mmul_1792, retro_mmul_1877, retro_mmul_2345,
Nomascus leucogenys	ENSNLEG00000000078	5 retrocopies	retro_nleu_1200, retro_nleu_1360 , retro_nleu_1654, retro_nleu_522, retro_nleu_561,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Pongo abelii	ENSPPYG00000004976	4 retrocopies	retro_pabe_2205, retro_pabe_2535, retro_pabe_2825, retro_pabe_3336,