RetrogeneDB ID: retro_nleu_1200

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:13516684..13517611(-)
• 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_1200
ATCCTGCCCTTTGATCATAGGGTTGTCCTACACAATGGTGATCCCAGTGAGGCTATTTTGGATTACATCAATGCAAATAT
CATCGTGCCTGAATTTGAAACCAAGTGCAACAATTCAAAGCCCAAAAAGAGTTACATTGCCACACAAGGCTGCCTGCAAA
ACACGGTGAACGACTTTTGGCAGATGGTGTTCCAAGAAAACTCCCAGGTGATTGTCATGACAACGAAAGAAGTGGAGAAA
GGAAAGAGTAAATGTGTCAAATACTGGCCTGATGAGTATGCTCTAAAAGAATACAGCATCATGCATGTTGGGAATGTCAA
AGAAAGTGCCGCTCATGACTATAAGCTAAGAGAACTTAAACTTTCAAAGGTTGGACAAGGGAATATGGAGAGAACGGTCT
GGCAATACCACTTTCAGACCTGGCTGTACCATGGAGTGCCCAGCGACCCCAAGGGCATGCTGCGCTTCCTGGACGAGGTG
TACCATAAGCAGGAGAGCATCATGGATGCAGGGCTGGTCGTGGTGCAGTGCAGTGCTGGCATTGGCCAGACAGGGACGTT
CATTGTGATTGATACTCTTATTGACATCATCAGAGAGAAAGGTGTTGACTGCGAAATTGACGTTCCCAAAACCATCCAGA
TGGTGCGGTCTCAGAGGTCAGAGATGGTCCAGACAGAAGCACAGTACCAATTTATCTATATGGCGGTCCAGCATCATATT
GAAACACTACAGCGCAAGACTGAGCAGAAAAGCAAGAGGAAAGGGCACGAATATACAAATATTAAGTATTCTCTAGTGGA
CCAGATGAGTGGAGATCAGAGCCCCCTCCTGCCTTATACTCCAATGCCACCCTGTGCAGAAATGAGAGAAGAGAGTGTTA
GAGTCTATGAAAACGTGGGCCTGATGCAACAGCAGAAAGATTTAAGA

Alignment

ORF - retro_nleu_1200 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.49 %
• Parental protein coverage: 61.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSR
          ILPFDH.RVVLH.GDP.E...DYINANII.PEFETKCNNSKPKKSYIATQGCLQNTVNDFW.MVFQENS.
Retrocopy ILPFDH-RVVLHNGDPSEAILDYINANIIVPEFETKCNNSKPKKSYIATQGCLQNTVNDFWQMVFQENSQ

Parental  VIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQALLQGNTERTVWQ
          VIVMTTKEVE.GKSKCVKYWPDEYALKEY..M.V.NVKESAAHDY.LRELKLSKVGQ....GN.ERTVWQ
Retrocopy VIVMTTKEVEKGKSKCVKYWPDEYALKEYSIMHVGNVKESAAHDYKLRELKLSKVGQ----GNMERTVWQ

Parental  YHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCD
          YHF.TW..HGVPSDP.G.L.FL.EV.HKQESIMDAG.VVV.CSAGIG.TGTFIVID.LIDIIREKGVDC.
Retrocopy YHFQTWLYHGVPSDPKGMLRFLDEVYHKQESIMDAGLVVVQCSAGIGQTGTFIVIDTLIDIIREKGVDCE

Parental  IDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQ
          IDVPKTIQMVRSQRS.MVQTEAQY.FIYMAVQH.IETLQR....EQKSKRKGHEYTNIKYSL.DQ.SGDQ
Retrocopy IDVPKTIQMVRSQRSEMVQTEAQYQFIYMAVQHHIETLQRK--TEQKSKRKGHEYTNIKYSLVDQMSGDQ

Parental  SPLPPCTPTPPCAEMREDSARVYENVGLMQQQKSFR
          SPL.P.TP.PPCAEMRE.S.RVYENVGLMQQQK..R
Retrocopy SPLLPYTPMPPCAEMREESVRVYENVGLMQQQKDLR

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_1200 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,