RetrogeneDB ID: retro_nleu_561

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:8391996..8393530(-)
• Located in intron of: ENSNLEG00000001356

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_561
ATAGAACATCACGGGCAATTAAAAGAGAAGAATGGAGATGTTATTCATCTTAAATATCCTCTGAACTGTGCAGATCCTAC
CTCTGAAAGGTGGTTTCAGGGACACCTCTCTGGGAAAGAAGCAGAGAAATTATTAACTGAAAAAGGAAAACATGTTAGTT
TTCTTGTACGAGAGAGCCAGAGCCACCTTGGAGATTTTGTTCTCTCTGTGTGCACCAGTGATGACAAAGGGGAGAGCAAT
AACGGCAAGTCTAAGGTGGCCCATGTTATGATTTGCTGTCAGGAACTGAAATACGATGTTGGTGGAGGAGAACAGTTTGA
TTCTTTGACAGATCTTGTGGAACATTACAAAAAGAATCCTATGGTGGAAACACTGGGTACAGTACTACAACTCAAGTAGC
CCCTTAACACAACTCGTATAAATGCTGCTGAAATAGAAAGCAGAGTTCGAGAACTAAGCAAATCAGCTGAGACCACAATA
AAGTCAAACAAGGCTTTTGGGAAGAATTTGAGACACTACAACAACAGGAGTGCAAACTTCTCTACAGCCGAAAAGAGGGT
CAAAGGCAAGAAAACAAAAACAAAAATAGATATAAAAACATCCTGCCCTTTGATCATACCAGGGTTGTCCTACACGGTGG
TGATCCCAATGAGCCTGTTTCAGATGACATCAATGCAAATATCATCATGCCCGAATTTGAAACCAAGTGTAACAATTCAA
AGCCCAAAAAGAGTTACATTGCTACACAAGGCTGCCTGCAAAACATGGTCAATGACTTTTGGCAGATGGTGTTCCAAGAA
AACTCCCGAGTGATTGTCATAACAACGAAAGAAGTGGAGAGAGGAAAGAGTAAATGTGTCAAATACCGGCCTGATGAGTA
TGCTCTGAAAGAATATGGCACCATGTGTGTTAAGAACGTCAGAGAAAGCGCCGCTCACAACTATATGCTAAGAGAACTTA
AACTTTCAAAGGTTGGACAAGGGAATATGGAGAGAATGGTCTGGCAATACCACTTTTGGACCTGGCCGGACCACGGAGTG
CCCACTGACCCTGGGGGTGTGCTGGACTTCCTGGAGAGGTGCACCATAAGCAGGAACGCATCATGCATGCAAGGCCAGTC
GTGGTGCACTGCAGTGCTGGAATTTGCCGGACAGGGACGTACGTTGTGACTGATACTCTGATTGGCATCATCAGAGAAAA
AGGTGTTGACTGTGACACTGACGTTCCCCAAACCATCCAGATGGTGCGGTCTCAGAGGTCAGGGATGGTCCAGACAGAAG
CACAGTACCGATTTATCTATATGGCGGTCCAGCATTATACTGAAACTCTACAGCACAGGATTGAAGAAGAGCAGAAAAGC
AAGAGGAAAGGGCATGAATATACAAATATTAAGTATTCTCTAGCGGACCAGATGAGTGGAGATCAGAGCCCCCTCCCGCC
TTGTACTCCAACTCCACGCTGTGCAGAAATGAGAGGAGACAGTGCTAGAGTCTATGAAAATGTGGGCCTGATGCAACAGC
AGAGGAGTTTCAGA

Alignment

ORF - retro_nleu_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSV
          .EHHGQLKEKNGDVI.LKYPLNCADPTSERWF.GHLSGKEAEKLLTEKGKH.SFLVRESQSH.GDFVLSV
Retrocopy IEHHGQLKEKNGDVIHLKYPLNCADPTSERWFQGHLSGKEAEKLLTEKGKHVSFLVRESQSHLGDFVLSV

Parental  RTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRI
          .T.DDKGESN.GKSKV.HVMI.CQELKYDVGGGE.FDSLTDLVEHYKKNPMVETLGTVLQLK.PLNTTRI
Retrocopy CTSDDKGESNNGKSKVAHVMICCQELKYDVGGGEQFDSLTDLVEHYKKNPMVETLGTVLQLK*PLNTTRI

Parental  NAAEIESRVRELSKLAETT-DKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRV
          NAAEIESRVRELSK.AETT..KVKQGFWEEFETLQQQECKLLYSRKEGQRQ...........LPFDHTRV
Retrocopy NAAEIESRVRELSKSAETT<NKVKQGFWEEFETLQQQECKLLYSRKEGQRQXXXXXXXXXXXLPFDHTRV

Parental  VLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV
          VLH.GDPNEPVSD.INANIIMPEFETKCNNSKPKKSYIATQGCLQN.VNDFW.MVFQENSRVIV.TTKEV
Retrocopy VLHGGDPNEPVSDDINANIIMPEFETKCNNSKPKKSYIATQGCLQNMVNDFWQMVFQENSRVIVITTKEV

Parental  ERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQALLQGNTERTVWQYHFRTWPDH
          ERGKSKCVKY.PDEYALKEYG.M.V.NV.ESAAH.Y.LRELKLSKVGQ....GN.ER.VWQYHF.TWPDH
Retrocopy ERGKSKCVKYRPDEYALKEYGTMCVKNVRESAAHNYMLRELKLSKVGQ----GNMERMVWQYHFWTWPDH

Parental  GVPSDPGGVLDFLE-EVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQ
          GVP.DPGGVLDFLE.EVHHKQE.IM.A.PVVVHCSAGI.RTGT..V.D.LI.IIREKGVDCD.DVP.TIQ
Retrocopy GVPTDPGGVLDFLE<EVHHKQERIMHARPVVVHCSAGICRTGTYVVTDTLIGIIREKGVDCDTDVPQTIQ

Parental  MVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTP
          MVRSQRSGMVQTEAQYRFIYMAVQHY.ETLQ.RIEEEQKSKRKGHEYTNIKYSLADQ.SGDQSPLPPCTP
Retrocopy MVRSQRSGMVQTEAQYRFIYMAVQHYTETLQHRIEEEQKSKRKGHEYTNIKYSLADQMSGDQSPLPPCTP

Parental  TPPCAEMREDSARVYENVGLMQQQKSFR
          TP.CAEMR.DSARVYENVGLMQQQ.SFR
Retrocopy TPRCAEMRGDSARVYENVGLMQQQRSFR

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_561 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,