RetrogeneDB ID: retro_nleu_1187

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:20305692..20306674(+)
• Located in intron of: ENSNLEG00000004679

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSNLEG00000011548
• Aliases: None
• Description: None

Sequence

>retro_nleu_1187
ATGAGTTTTCTTGACGGCTTTTTTGGTCCAATTTGTGAGATCGATATTGTCTTTAATGATGGGGAAGCCAGGAAAATGAC
AGAAATGAAAACTGAAGATGGCAAAGTAGAAAAACACCATCTCTTTGTAACGGAGAATCTGTTTCAGGTAAGGTAAACGT
GGCCTTTAAGCAACCTGGATAGAGGCTAGAACACCAAGGAATTAGAATTGAATTTGTAGGTCAAATGGAACTTTACAATG
AGAAGAGTAATGCTCATGAATTTATAAACCTAATGAAAGAACTAGCCTTACCTGGAGAACTGACTCAGAGAAGAAGTTAT
GATTCTGTATTTATGCAAGTTGAAAAGCCATATGCATCTGACATTGGCGCCAATGTTCACTTGAGGAATTTTCTTAAAGT
GACAATAGTGAGAAGACTGACAGATTTAGTAAAAGAATATGATCTTACTGTTCACCAGCTTGCCACCTGTCCTGATGTTA
ACAACTGTATTAAGATAGAAGTGGGCATTGAAGATTGTCTACATATATAATTTGAATATAATAAGTCAAAGTATCATTTA
AAGCATGTAATTGTTGGAAACATTTACTTCTTAGTAGTAAGAATAAAAGTACAACATATGGAGTTACAACTGATCAAAAA
AGAGATCACAGGAATTGGACCCAGTACCACAGCAGAAACAGAAACAATCACCAAATATGAAATAATAGATGGTGCACCAG
TAAAAGGTGAATCAATTCCAATGAGACTATTTTTAGCGGGATATGACCCTACTCCAACAATCAGAGAGATGTGAACAAAA
AAGTTTCAGTAAGGTACTTTATGAATTTAGTGTTTGTTGATGAGGAAGACTGAAGGTACTTTAAACAGCAGGAGATCATT
TTATGAAGAAAAGCTCCTGAAAAACTGAGGAAACAGAGAAAAAACTTTCACCAGTAATTTGAATCTCCACAATCGCAGGC
ATCTGCTGAACAGCCTGAAATG

Alignment

ORF - retro_nleu_1187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFY-DGESVSGKVNLAFKQPGKRLEHQGIR
          MSFL.GFFGPICEIDIV.NDGE.RKM.EMKTEDGKVEKH.LF...GESVSGKVN.AFKQPG.RLEHQGIR
Retrocopy MSFLDGFFGPICEIDIVFNDGEARKMTEMKTEDGKVEKHHLFV<NGESVSGKVNVAFKQPG*RLEHQGIR

Parental  IEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRR
          IEFVGQ.EL.N.KSN.HEF.NL.KELALPGELTQ.RSYD..FMQVEKPY.S.IGANV.LR.FLKVTIVRR
Retrocopy IEFVGQMELYNEKSNAHEFINLMKELALPGELTQRRSYDSVFMQVEKPYASDIGANVHLRNFLKVTIVRR

Parental  LTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMEL
          LTDLVKEYDL.VHQLAT.PDVNN.IK.EVGIEDCLHI.FEYNKSKYHLK.VIVG.IYFL.VRIK.QHMEL
Retrocopy LTDLVKEYDLTVHQLATCPDVNNCIKIEVGIEDCLHI*FEYNKSKYHLKHVIVGNIYFLVVRIKVQHMEL

Parental  QLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDV-NKKF-SVRYFLNLV
          QLIKKEITGIGPSTT.ETETI.KYEI.DGAPVKGESIP.RLFLAGYDPTPT.R....KKF.SVRYF.NLV
Retrocopy QLIKKEITGIGPSTTAETETITKYEIIDGAPVKGESIPMRLFLAGYDPTPTIREM*TKKF<SVRYFMNLV

Parental  LVDEEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM
          .VDEED.RYFKQQEIIL.RKAPEKLRKQR.NFHQ.FESP.SQASAEQPEM
Retrocopy FVDEED*RYFKQQEIIL*RKAPEKLRKQRKNFHQ*FESPQSQASAEQPEM

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_1187 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013827	1 retrocopy	retro_cfam_1133,
Choloepus hoffmanni	ENSCHOG00000007324	5 retrocopies	retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352, retro_chof_242,
Callithrix jacchus	ENSCJAG00000012907	1 retrocopy	retro_cjac_1420,
Equus caballus	ENSECAG00000009507	1 retrocopy	retro_ecab_17,
Homo sapiens	ENSG00000122958	1 retrocopy	retro_hsap_2688,
Gorilla gorilla	ENSGGOG00000010433	1 retrocopy	retro_ggor_1875,
Microcebus murinus	ENSMICG00000014940	1 retrocopy	retro_mmur_1070,
Mustela putorius furo	ENSMPUG00000004519	1 retrocopy	retro_mputfur_146,
Nomascus leucogenys	ENSNLEG00000011548	1 retrocopy	retro_nleu_1187 ,
Pongo abelii	ENSPPYG00000002386	1 retrocopy	retro_pabe_2293,
Pan troglodytes	ENSPTRG00000002567	3 retrocopies	retro_ptro_1815, retro_ptro_2245, retro_ptro_4,
Tupaia belangeri	ENSTBEG00000015348	1 retrocopy	retro_tbel_1425,
Vicugna pacos	ENSVPAG00000000630	1 retrocopy	retro_vpac_385,