RetrogeneDB ID: retro_nleu_2146

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397331.1:9780644..9781523(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000004809
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPPL2B
• Ensembl ID: ENSNLEG00000011710
• Aliases: None
• Description: None

Sequence

>retro_nleu_2146
GAAGATAATGAGGACATCCCAGTGGACTTCACGCCGGCCATGACAGGCGTGGTGGTCACCCTGTCCTGCTCGATCATGCT
GCTGCTCTACTTCTTCTATGACCACTTTGTCTATGTCACCATCGGGATCTTTGGCCTGGGTGCTGGCATTGGCCTCTACA
GCTGCCTGTCACCCCTGGTGCGCCGCCTGTCCCTGCGGCAGTACCAGAGGCCTCCGCATGGCCTCTGGGCCTCTCTGCCG
CTGCCTCTGCTGCTGCTGGCGAGCCTGTGCACAACCGTGATCGTCTTCTGGATGGCCTACCGCCACGAGGACCGCTGGGC
GTGGCTTCTGCAGGACACACTGGGCATTTCCTACTGCCTGTTCGTCCTGCACCGTGTGCGGCTGCCCACTCTCAAGAACT
GCTCCTCCTTCCTGCTGGCCCTGCTGGCCTTTGATGTCTTCTTTGTCTTCGTCACCCCCTTCTTCACCAAAACCGGTGAG
AGCATCATGGCGCAGGTTGCCTTGGGCCCTGCAGAGTCTTCAAGCCACGAGAGGCTGCCCATGGTGCTCAAAGTGCCCCG
GCTAAGAGTCTCCGCCTTGACCCTGTGCAGCCAGCCCTTCTCCATCCTTGGCTTCGGTGACATCGTGGTCCCCGGCTTCC
TGGTTGCTTACTGTTGCCGCTTCGATGTGCAAGTCCACTCCCGTCAGGTCTACTTCGTGGCCTGCACCGTGGCCTATGCT
GTGGGCCTGCTGGTCACATTCATGGCCATGGTCCTCATGCAGATGGGCCAACCTGCCTTGCTCTACCTCGTGTCCAGCAC
CCTGCTCACCAGCCTGGCTGTGGCTGCCTGCCGCCAAGAGCTCAGCCTCTTCTGGACTGGCCAGGGCAGAGCTAAGATG

Alignment

ORF - retro_nleu_2146 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.12 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKQEDEAVDVTPVMTCVFVVMCCSMLVLLYYFYDLLVYVVIGIFCLASATGLYSCLAPCVRRLPFGKCRI
          E..ED..VD.TP.MT.V.V...CS...LLY.FYD..VYV.IGIF.L....GLYSCL.P.VRRL.......
Retrocopy EDNEDIPVDFTPAMTGVVVTLSCSIMLLLYFFYDHFVYVTIGIFGLGAGIGLYSCLSPLVRRLSLRQYQR

Parental  PNNSLPYFHKRPQARMLLLALFCVAVSVVWGVFRNEDQWAWVLQDALGIAFCLYMLKTIRLPTFKACTLL
          P...L......P....LL..L.C..V.V.W...R.ED.WAW.LQD.LGI..CL..L...RLPT.K.C...
Retrocopy PPHGL--WASLPLPLLLLASL-CTTVIVFWMAYRHEDRWAWLLQDTLGISYCLFVLHRVRLPTLKNCSSF

Parental  LLVLFLYDIFFVFITPFLTKSGSSIMVEVATGPSDSATREKLPMVLKVPRLNSSPLALCDRPFSLLGFGD
          LL.L...D.FFVF.TPF.TK.G.SIM..VA.GP..S...E.LPMVLKVPRL..S.L.LC..PFS.LGFGD
Retrocopy LLALLAFDVFFVFVTPFFTKTGESIMAQVALGPAESSSHERLPMVLKVPRLRVSALTLCSQPFSILGFGD

Parental  ILVPGLLVAYCHRFDIQVQSSRVYFVACTIAYGVGLLVTFVALALMQRGQPALLYLVPCTLVTSCAVALW
          I.VPG.LVAYC.RFD.QV.S..VYFVACT.AY.VGLLVTF.A..LMQ.GQPALLYLV..TL.TS.AVA..
Retrocopy IVVPGFLVAYCCRFDVQVHSRQVYFVACTVAYAVGLLVTFMAMVLMQMGQPALLYLVSSTLLTSLAVAAC

Parental  RRELGVFWTGSGFAKV
          R.EL..FWTG.G.AK.
Retrocopy RQELSLFWTGQGRAKM

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_2146 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000011710	1 retrocopy	retro_nleu_2146 ,
Procavia capensis	ENSPCAG00000011127	1 retrocopy	retro_pcap_285,
Pelodiscus sinensis	ENSPSIG00000017155	1 retrocopy	retro_psin_63,