RetrogeneDB ID: retro_nleu_268

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:3064796..3065549(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG3
• Ensembl ID: ENSNLEG00000004302
• Aliases: None
• Description: Autophagy-related protein 3 [Source:UniProtKB/TrEMBL;Acc:G1QWE6]

Sequence

>retro_nleu_268
TTGATTAATATGGTGAAAGAAAGGCACTAGAAGTAACTGAATACCTGACCTAATTCTCAAGGAATCAGTTTAAGGACACA
GCTGTTATCACCCCAAAAGAGTTTATAGCAGCTGGAGATCACTTAGCTGTCCACTGCCCAACACAGCAATGGGCTACAGG
GGAAGAACTGGAAAGAGGCATAGCTACCAACAGGCAAATAATTTTTGGTAGCCAAAAATGTGGCATGCTACATCCAGTCA
AAACAGACAGCATATTCAGGTGAATTGGAAGCTATCACTGAAGATGATGGTGGTAGGGCATGGGTAGATACACATCACAG
CACAGGAATTGCAGGAATAAACAAATAGGTTGAGGAGATTATACCTATAAGCAAAAATGGTATAAAACTCCAAAACTGCT
CAGCCTTATGAGAGGAAGAAGAAAAAGATGAAGGAAAATCTACATTTATGGAATAATATGAAGAGAGTGGGTTGCTGGAA
GCAGACAAAGCTACCCCAGATGAAAGGAAAATAGTAGAAGCTTGTAAAGCTTAAAGTGATGTTGGAGGTGAAGATGCTCT
TTTGCAAACCAAAACTTGCGACCTTTACATCATATATGGTAAATATTACCAGACGGCACAACTATGGTTTTTTGGCTATG
ATGGGGAACAGCAGATTTTCACAGCTGAACACATGTATAAAGACATCATTCAAGACCATATGAAGAAAACAGTGACCACT
GAAAGTCCCTCCACCAATCTCCCTCCACCTCCT

Alignment

ORF - retro_nleu_268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.81 %
• Parental protein coverage: 80.89 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VINTVKG-KALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWAT-GEELKVKAYLPTGK
          .IN.VK..KALEV.EYLT.......FK.T.VITP.EF.AAGDHL..HCPT.QWAT.G...K..A.LPTGK
Retrocopy LINMVKE<KALEVTEYLT*-FSRNQFKDTAVITPKEFIAAGDHLAVHCPTQQWAT>GKNWK-EA*LPTGK

Parental  QFLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNTGITGITEAVKEITLENKDNIRLQDCSA
          .FLV.KNV.CY...KQ..YS.ELEAI.E.DDG...WVDT.H.TGI.GI...V.EI....K..I.LQ.CSA
Retrocopy *FLVAKNVACYIQSKQTAYSGELEAITE-DDGGRAWVDTHHSTGIAGINK*VEEIIPISKNGIKLQNCSA

Parental  LCEEEEDEDEGEAADMEEYEESGLLETDEATLDTRKIVEACKAKTDAGGEDAILQTRTYDLYITYDKYYQ
          L.EEEE..DEG....ME.YEESGLLE.D.AT.D.RKIVEACKA..D.GGEDA.LQT.T.DLYI.Y.KYYQ
Retrocopy L*EEEE-KDEGKSTFME*YEESGLLEADKATPDERKIVEACKA*SDVGGEDALLQTKTCDLYIIYGKYYQ

Parental  TPRLWLFGYDEQRQPLTVEHMYEDISQDHVKKTVTIEN-HPHLPPPP
          T..LW.FGYD...Q..T.EHMY.DI.QDH.KKTVT.E.....LPPPP
Retrocopy TAQLWFFGYDGEQQIFTAEHMYKDIIQDHMKKTVTTESPSTNLPPPP

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_268 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.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018116	1 retrocopy	retro_amel_645,
Callithrix jacchus	ENSCJAG00000020358	1 retrocopy	retro_cjac_2756,
Equus caballus	ENSECAG00000011954	1 retrocopy	retro_ecab_594,
Homo sapiens	ENSG00000144848	1 retrocopy	retro_hsap_2479,
Gorilla gorilla	ENSGGOG00000006637	1 retrocopy	retro_ggor_1544,
Myotis lucifugus	ENSMLUG00000001573	1 retrocopy	retro_mluc_1025,
Macaca mulatta	ENSMMUG00000014232	1 retrocopy	retro_mmul_594,
Mustela putorius furo	ENSMPUG00000000321	2 retrocopies	retro_mputfur_1064, retro_mputfur_1614,
Nomascus leucogenys	ENSNLEG00000004302	2 retrocopies	retro_nleu_268 , retro_nleu_331,
Oryctolagus cuniculus	ENSOCUG00000015651	1 retrocopy	retro_ocun_1219,
Pongo abelii	ENSPPYG00000013548	1 retrocopy	retro_pabe_1827,
Pan troglodytes	ENSPTRG00000015220	1 retrocopy	retro_ptro_1434,
Pteropus vampyrus	ENSPVAG00000009568	1 retrocopy	retro_pvam_1399,