RetrogeneDB ID: retro_nleu_1949

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397318.1:2395306..2395969(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSNLEG00000004229
• Aliases: None
• Description: None

Sequence

>retro_nleu_1949
ATAGAAATCTCATGGACCCATGACCCAGCCTCCAAGGCAGCCTCGGTGGCAGTGAACTACCTCAACTACCAGCAGGGGAC
ACTCCACAAGGTATTTCTGAGGCAGACAGTCAAACAAGCTAGGACGGAAGATATTCCGGGAAAAGGACATAAGTATCACC
TCAAATGTTCTGTGGAATAAGTCATTCTAAAACAAGTTACAGTGAACTGCATAGCTGAATTGCCTTACCCTGCAGTGGGA
CAAGATACTGCACCAGAAATCAACATCACATGTGAAGGAGAAATGGAAAGAGCCCAGAGGAAGAAAACAACACATCTGAT
CAAAAACTCAAGTCCGTGAAGGAATCACTAGAAGCACAAAATATTCCAGACATTTTGAGAAATGTATCTCCAAAACATGA
AGCCAGGTCAACATTTAGCCTGGGTTGCCTGTGGTTATATAACATGGTAAAATTCTACTGAAAACACATGATATAAAAGT
GGTAAAAATTAAACTGTCAAGGAAATGCAAAAAAATGACTTTATCGAATAGACTATACCATTCCACTTCATGACATTGCA
TCCCAGGAGATTGATTCCTTGGCAAATGCAAGTTCTTTGGCACTGACAAGATGGTGCTAAAGTAAAATGTAATCGCTGTG
TGCCAAGGGAAGTACAAGTGGAA

Alignment

ORF - retro_nleu_1949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNC
          .EI..T..PAS.AA.VA.NY.NYQQGT.H.VF..Q.VKQA..EDIPG.GHKY.LK..VE..I.KQV.VNC
Retrocopy IEISWTHDPASKAASVAVNYLNYQQGTLHKVFLRQTVKQARTEDIPGKGHKYHLKCSVE*VILKQVTVNC

Parental  TAEVLYPSTGQETAPEVNFTFEGE-TGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPE-MTLVLH
          .AE..YP..GQ.TAPE.N.T.EGE..GK.P.EE.NT..Q.LKS.KE.LEAQNIPD...NVSP..M....H
Retrocopy IAELPYPAVGQDTAPEINITCEGE<NGKSPEEENNTSDQKLKSVKESLEAQNIPDILRNVSPK>MKPGQH

Parental  LAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIE-LDYTILLHNIASQEI-IPWQMQVLWHPQYG
          LAWVACGYI.W.NSTE.T.YK..K..TVK..Q.N.DFIE..DYTI.LH.IASQEI.IPWQMQVLWH.Q.G
Retrocopy LAWVACGYITW*NSTENT*YKSGKN*TVKEMQKN-DFIE<IDYTIPLHDIASQEI>IPWQMQVLWH*QDG

Parental  TKVKHNSRLPKEVQLE
          .KVK.N...P.EVQ.E
Retrocopy AKVKCNRCVPREVQVE

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_1949 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009336	2 retrocopies	retro_btau_569, retro_btau_860,
Canis familiaris	ENSCAFG00000009096	1 retrocopy	retro_cfam_1863,
Callithrix jacchus	ENSCJAG00000000386	1 retrocopy	retro_cjac_1890,
Homo sapiens	ENSG00000079257	1 retrocopy	retro_hsap_3397,
Gorilla gorilla	ENSGGOG00000003092	1 retrocopy	retro_ggor_2300,
Macaca mulatta	ENSMMUG00000004963	1 retrocopy	retro_mmul_2114,
Nomascus leucogenys	ENSNLEG00000004229	1 retrocopy	retro_nleu_1949 ,
Pongo abelii	ENSPPYG00000014245	1 retrocopy	retro_pabe_2791,
Pan troglodytes	ENSPTRG00000015571	1 retrocopy	retro_ptro_2308,
Pteropus vampyrus	ENSPVAG00000013608	2 retrocopies	retro_pvam_94, retro_pvam_962,
Tupaia belangeri	ENSTBEG00000017673	3 retrocopies	retro_tbel_2746, retro_tbel_3329, retro_tbel_4516,