RetrogeneDB ID: retro_nleu_436

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:22330561..22331274(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSNLEG00000004516
• Aliases: None
• Description: None

Sequence

>retro_nleu_436
GACAGTATGGCTGTGGCATTTTGGTCCTCCAGATGAGCTCTTCTGCCAGCGCTGCAGATTTCAGTGTATCCCGGGATGAG
AGGCTCCGGCTCCACTTGCTGCCACAGTCCTCTTGGAGCAAAAAGATATCTACTTACAGATAATATTGTGAAATTAAAAG
AATTTCAGCATAAGAAGGTGGCTGTTGCATATAATCTTCCTGGCACCAAAGAAATCTATTTTAGAAACTTGGAAGAGAAA
TTGAACTAGAACAAGCTCATCTTGAAGGGGAAGTTAAGAACCCTACTTCATTTGCGTGAGTCCTGGGACCATGTGGAACT
GGCTAAAAACGTCACTTGCAAGTACCATACAGAAAACAAAAATGTCACTTTGGCGGAATTTAAGTTTGGACCACTTTTCA
TAAGACTGTGTTACGACTCGAATCTTGAGGAATCTGCAATGGAGCTCATGAAAGATGAGTATTTACAAGGGTTCTCAGAC
TCCACACAATTTACTATTTTGATGGTTATGTTATTTATCAAAAGCAAATATGTAAGTGCTTTGGAAATATTGACAGAGAT
GAAAAACTCAGATATAAAGTTCACCAGGATACCTATGTTCTTGATTTTGCAATTGGCTACAAACTGAATAGCTCTGAATC
TTTCGAAGTCTGTACTACATGAAGAAAAGAAGCCTTAATCAAAGGAGTTCTCTCCAGGAGGTCATCCTGTTTC

Alignment

ORF - retro_nleu_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.2 %
• Parental protein coverage: 61.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSMAAALRPSNRVLLQALQILVYPGVGGSGSVSCRCPFGAKRYLLTDNVVKLKEFQQKKVAVACNLSGTK
          DSMA.A...S...LL.ALQI.VYPG..GSGS..C..P.GAKRYLLTDN.VKLKEFQ.KKVAVA.NL.GTK
Retrocopy DSMAVAFWSSR*ALLPALQISVYPGMRGSGSTCCHSPLGAKRYLLTDNIVKLKEFQHKKVAVAYNLPGTK

Parental  ETYFRNLKEKLTQNKLILKGELITLLHLCESRDHVELAKNVIYRYHAENKNFTLGEYKFGPLFVRLCYEL
          E.YFRNL.EKL..NKLILKG.L.TLLHL.ES.DHVELAKNV...YH.ENKN.TL.E.KFGPLF.RLCY..
Retrocopy EIYFRNLEEKLN*NKLILKGKLRTLLHLRESWDHVELAKNVTCKYHTENKNVTLAEFKFGPLFIRLCYDS

Parental  DLEESAVELMKDQHLRGFFSDSTSFNILMDMLFIKGKYKSALEVLIEMKNQDVRFTK-DTYVLAFAICYK
          .LEESA.ELMKD..L.G.FSDST.F.ILM.MLFIK.KY.SALE.L.EMKN.D..FT..DTYVL.FAI.YK
Retrocopy NLEESAMELMKDEYLQG-FSDSTQFTILMVMLFIKSKYVSALEILTEMKNSDIKFTR<DTYVLDFAIGYK

Parental  LNSPESFKICTTLREEALLKGEILSRRASCF
          LNS.ESF..CTT.R.EAL.KG..LSRR.SCF
Retrocopy LNSSESFEVCTT*RKEALIKG-VLSRRSSCF

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_436 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436 ,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,