RetrogeneDB ID: retro_nleu_522

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397266.1:29491713..29493241(-)
• 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_522
ATGGAATATCACAGCAATTCGAAGAGAAGAATGGAGATGTTATTGAGCTTAAATATCCTCTGAACTGTGCAGATCCTACC
TCTGAAAGATGGTTTCATGGACACCTCTTTGGGAAAGAAGCAGAGAAATTAACTGAAAAAGGAAAACATGGTAGCTTTCT
TATACGAGAGAGCCAGAGCCACCCTGGAGATTTTGTTCTCTCTGCGCGCACCAGTGATGACAAAAGGGAGAGCAATGACA
GCAAGTCTAAAGTGACCCATGTCATGATTCGCTGTCAGGAACTGAAATACGTTGGTGGAGGAGAACTGTTTGATTCTTTG
ACGGATCTTGTGGAACATTACAAGAAGAATCCTATGCTGGAAACATTGGGTACAGTGCTACGACTCAAGTAGCCCCTTAA
CAGGACTTGTATAAATGCTGCTGAGATAGAAAGCAGAGTTTGAGAACTAAGCAAATTAGCTGAGACCACAGATAAAGTCC
AACAAGGCTTTTGGGAAGAATTTGAGACACTACAACCACAGGCGTGCAAACTTCTCTACAGCAGAAAAGAGGGTCAAAGG
CAAGAAAACGAAAACAAAAATAGATATAAAAACTTCCTGCCCTTTGATCATACCAGGGTTGTCCTGCACGATGGTGATCC
CAACGAGCCTATTTCAGATGACATCAATGCAAATATCATCATGCCTGAATTTGAAACCAAGTGCAACAATTCACAGCCCA
AAAGGAGTTGCATTGCCACACAAGGCTGCCTGCAAAACACGGTGAATGACTTTTGCTGGATGGTGTTCCAAGAAAACTCC
CAAGTGATTGTCACGACAACAAAAGAAATGGAGAGAGGAAAGAGTAAATGTGTCAAATACTGGTCTGATGAAGATGCTGT
ACAAGAATATGGGGTATGCGTGTTAGGAACATCAAAGAAAGTGCTGCTCATGACTATATGCTAAGAGAACTTAAATTTTC
AAAGGTTGGACAAGCTCTATTCCAGCGGAATATGGAGAGTACGGTCTGGCAATACCACTTTCGGACCTGACCAGACCACG
GAGTGCCCAGCGACCCCGGAGGCATGCTGGACTTCCTGGAGGAGGTGCACCATAAGCAGGAGAGCACCATGGATGAGGGC
CGGTCGTGGTCCACTGCAGTACTGGAAATGGCCATACAGGGATGTTCATTGTGATTAATAGTCTTATTGACATCATCAGA
GAGAAAAGTATTAACTGCGACATTGACCTTGTCAAAACCATCCACACAGTGCAGTCTCAGAGGTCAGGGATGGCCCAGAC
AGAAGCACAGTACCGATTTATCTATATGGCAGTCCAGCATTATACTGCAACACTACAGCACAGGATTGAAGAAGAGCAGA
AAAGCAAGAGGAAAGGGCACGAATATACAAATATTAAGTATTCTCTAGCGGATCAGACGAGTGGAGCTCACAGCGCCCCC
CCCACCTTTCACTCCAGCGCCACCCTGTGCAGAAATGAGAGAAGACACTGCTGCAGTCTATGAAAACGTGGGCCTGATGC
AACAGAAA

Alignment

ORF - retro_nleu_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEHHG-QLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLS
          ME.H..Q..EKNGDVIELKYPLNCADPTSERWFHGHL.GKEAEKL.TEKGKHGSFL.RESQSHPGDFVLS
Retrocopy MEYHS<QFEEKNGDVIELKYPLNCADPTSERWFHGHLFGKEAEKL-TEKGKHGSFLIRESQSHPGDFVLS

Parental  VRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTR
          .RT.DDK.ESND.KSKVTHVMIRCQELKY.VGGGE.FDSLTDLVEHYKKNPM.ETLGTVL.LK.PLN.T.
Retrocopy ARTSDDKRESNDSKSKVTHVMIRCQELKY-VGGGELFDSLTDLVEHYKKNPMLETLGTVLRLK*PLNRTC

Parental  INAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRV
          INAAEIESRV.ELSKLAETTDKV.QGFWEEFETLQ.Q.CKLLYSRKEGQRQEN.NKNRYKN.LPFDHTRV
Retrocopy INAAEIESRV*ELSKLAETTDKVQQGFWEEFETLQPQACKLLYSRKEGQRQENENKNRYKNFLPFDHTRV

Parental  VLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV
          VLHDGDPNEP.SD.INANIIMPEFETKCNNS.PK.S.IATQGCLQNTVNDF..MVFQENS.VIV.TTKE.
Retrocopy VLHDGDPNEPISDDINANIIMPEFETKCNNSQPKRSCIATQGCLQNTVNDFCWMVFQENSQVIVTTTKEM

Parental  ERGKSKCVKYWPDEYALKEYGV-MRVRNVKESAAHDYTLRELKLSKVGQALLQGNTERTVWQYHFRTWPD
          ERGKSKCVKYW.DE.A..EYGV.MRVRN.KESAAHDY.LRELK.SKVGQAL.Q.N.E.TVWQYHFRT.PD
Retrocopy ERGKSKCVKYWSDEDAVQEYGV<MRVRNIKESAAHDYMLRELKFSKVGQALFQRNMESTVWQYHFRT*PD

Parental  HGVPSDPGGVLDFLEEVHHKQESIMDA-GPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTI
          HGVPSDPGG.LDFLEEVHHKQES.MD..GPVVVHCS.G.G.TG.FIVI..LIDIIREK...CDID..KTI
Retrocopy HGVPSDPGGMLDFLEEVHHKQESTMDE<GPVVVHCSTGNGHTGMFIVINSLIDIIREKSINCDIDLVKTI

Parental  QMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQS-PLPPC
          ..V.SQRSGM.QTEAQYRFIYMAVQHY..TLQ.RIEEEQKSKRKGHEYTNIKYSLADQTSG..S....P.
Retrocopy HTVQSQRSGMAQTEAQYRFIYMAVQHYTATLQHRIEEEQKSKRKGHEYTNIKYSLADQTSGAHS>XXXPF

Parental  TPTPPCAEMREDSARVYENVGLMQQQ
          TP.PPCAEMRED.A.VYENVGLMQQ.
Retrocopy TPAPPCAEMREDTAAVYENVGLMQQK

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_522 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,