RetrogeneDB ID: retro_nleu_1654

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397302.1:14628619..14629561(-)
• 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_1654
AAAAACATCCTGCCCTTTGATCATATCAGGGTTGTTCTACATGACAGTGATCCCAATGAGACTGTTTCAGATTACATCAA
TGCAAGTATCATCATGCCTGAATTTGAAACCAAGTGCAACAATTCAAAGCCCAAAAAGAGTTACATTGCCACACAAGGCT
GCCTGCAAACCACAGTGAACGACTTTTGGCGGATGGTGTTCCAAGAAAACTCTGGAGTGATTGTCATGACAATGAAAGAA
GTGGAGAGAGGAAAGAGTAAATGTGTCAAACACTGGCCTGATGAGTATGCTCTAAAAGAATATGGTGTCATGCTTGTTAG
GAACGTCAGAGAAAGCACTGCTCATGACTATACGCTAAGAAAACTTAAACTTTCAAATGTTGGACAAGGGAATACGGAGA
GAACAGTCTGGCAATACCACTTTCAGATCTGGCTGGACCACAGAGTGCTCAGCAACCCCGGGGTTGTGCTGGACCTCCCG
GAGAAGGTGCACCACAAGCGGGAGAGCACCATGGATGCAGGGCTGGTCGTGGTGCACTGCAGTGCTGGAATTGGCCGGAC
AGGGATGGTCATTGTGATTGATATTCTTATTGACATCATCAGAGAGAAAGGTGTTGACTGCGACATTGATGTTCCCCAAA
CCATCCAGATGGTGTGGTCTAAGAGGTAAGGGATGGTCCAGACAGAAGCACTGTACCAATTTATCTATATGGCGGTCCAG
CGTTATATTGAAACACTACAGCTCAGGATTGAACAAAAGCAGAAAAGCAAGAGGAAAGGGCAGGAATATATAAATATTAA
GTATTCTCTAGCGGACCAGATGAGTGGAAATCAAAGCCCCCTCCCACCTTATACTCCAAAGCCACCCTGTGCAGAAATGA
GAGAAGACAGTGCTAGAGTCTATGAAAACGTGGGCCTGATGCAACAGCAGAAAAGTTTCAGA

Alignment

ORF - retro_nleu_1654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.91 %
• Parental protein coverage: 61.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQEN
          KNILPFDH.RVVLHD.DPNE.VSDYINA.IIMPEFETKCNNSKPKKSYIATQGCLQ.TVNDFWRMVFQEN
Retrocopy KNILPFDHIRVVLHDSDPNETVSDYINASIIMPEFETKCNNSKPKKSYIATQGCLQTTVNDFWRMVFQEN

Parental  SRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQALLQGNTERTV
          S.VIVMT.KEVERGKSKCVK.WPDEYALKEYGVM.VRNV.ES.AHDYTLR.LKLS.VG....QGNTERTV
Retrocopy SGVIVMTMKEVERGKSKCVKHWPDEYALKEYGVMLVRNVRESTAHDYTLRKLKLSNVG----QGNTERTV

Parental  WQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVD
          WQYHF..W.DH.V.S.PG.VLD..E.VHHK.ES.MDAG.VVVHCSAGIGRTG..IVIDILIDIIREKGVD
Retrocopy WQYHFQIWLDHRVLSNPGVVLDLPEKVHHKRESTMDAGLVVVHCSAGIGRTGMVIVIDILIDIIREKGVD

Parental  CDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSG
          CDIDVP.TIQMV.S.R.GMVQTEA.Y.FIYMAVQ.YIETLQ.RIE..QKSKRKG.EY.NIKYSLADQ.SG
Retrocopy CDIDVPQTIQMVWSKR*GMVQTEALYQFIYMAVQRYIETLQLRIEQKQKSKRKGQEYINIKYSLADQMSG

Parental  DQSPLPPCTPTPPCAEMREDSARVYENVGLMQQQKSFR
          .QSPLPP.TP.PPCAEMREDSARVYENVGLMQQQKSFR
Retrocopy NQSPLPPYTPKPPCAEMREDSARVYENVGLMQQQKSFR

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_1654 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,