RetrogeneDB ID: retro_nleu_467

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:27459884..27460393(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11A
• Ensembl ID: ENSNLEG00000012853
• Aliases: None
• Description: None

Sequence

>retro_nleu_467
TTTGCAACAAGAAGCATCCAGATTGATAGGAAAACAATAAAGGCACAGATGTGGGACAGAGCAGGGCAAGAGTAATACCA
AGCTATAACATTAGCATATTATCATGGAGATGTAGGTGCCTTATTGGTTTAAGACATTGCTAAACATCTCACATATGAAA
ATACAGAATGATTGCTGAAAGAACTGAGCAATTACACTGATAGTAACATTGTTGTCATGTTATCATGGACAAATAAGAGT
GATTTACATCATCTCAGGGAAGTTCCTAGAGTTGAAGCAAGAGCTTTGGCAGAAAAAATGATTTGTCATTCATTGAGACA
TCTGCTCTAGACTCTACAAATGTAGAAGCTACTTTTCAGGCAATTCTAACAGAGATACCTCACATTGTTTCTCAGAGGCA
AATGTCAGACAGAGCCGAAAATGACATGTCCCCAAGCAATAATGTGGTTCCTATGAATGTTCCACCAATCACTGAAAACA
AACCAAAGGTGCAGGGCTGTCAGAACATC

Alignment

ORF - retro_nleu_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 64.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
          FATRSIQ.D.KTIKAQ.WD.AGQE.Y.AIT.AYY.G.VGALLV.DIAKHLTYEN.E..LKEL....DSNI
Retrocopy FATRSIQIDRKTIKAQMWDRAGQE*YQAITLAYYHGDVGALLV*DIAKHLTYENTE*LLKELSNYTDSNI

Parental  VIMLVG-NKSDLRHLRAVPTDEARAFAEK-NGLSFIETSALDSTNVEAAFQTILTEIYRIVSQKQMSDRR
          V.ML...NKSDL.HLR.VP..EARA.AEK.N.LSFIETSALDSTNVEA.FQ.ILTEI..IVSQ.QMSDR.
Retrocopy VVMLSWTNKSDLHHLREVPRVEARALAEK<NDLSFIETSALDSTNVEATFQAILTEIPHIVSQRQMSDRA

Parental  ENDMSPSNNVVPIHVPPTTENKPKVQCCQNI
          ENDMSPSNNVVP..VPP.TENKPKVQ.CQNI
Retrocopy ENDMSPSNNVVPMNVPPITENKPKVQGCQNI

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_467 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018959	1 retrocopy	retro_btau_1850,
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Homo sapiens	ENSG00000103769	1 retrocopy	retro_hsap_715,
Gorilla gorilla	ENSGGOG00000014252	2 retrocopies	retro_ggor_538, retro_ggor_605,
Myotis lucifugus	ENSMLUG00000008820	2 retrocopies	retro_mluc_1606, retro_mluc_2435,
Macaca mulatta	ENSMMUG00000008006	1 retrocopy	retro_mmul_2463,
Nomascus leucogenys	ENSNLEG00000012853	1 retrocopy	retro_nleu_467 ,
Nomascus leucogenys	ENSNLEG00000014339	1 retrocopy	retro_nleu_2062,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pan troglodytes	ENSPTRG00000007188	1 retrocopy	retro_ptro_510,