RetrogeneDB ID: retro_nleu_331

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:46812650..46813505(+)
• Located in intron of: ENSNLEG00000007004

Retrocopy information

• Ensembl ID: ENSNLEG00000007009
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_331
CCCCGGTCCTCAAGGAATCAGTTTAAGGAAACAGGTGTAATCACCCCAGAAGAGTTTGTGGCAGCTGGAAATAACATAGT
CCACCACTGTCCAACATGGCAATGGGCTACAGGGGAAGAATTGAAAGTGAAGGGATACCTACCCACAGGCAAACAATTTT
TGGTAACCAAAAATGTGCTGTGCTATAAGCCGTGCAAACAGATGGAATATTCAGAGGAATTGGAAGCTATCATTGAAGAA
GAGGATGGTGATGGCGGATGGGTAGATACACATCATAACACAAGCATTACAGGAATAACGGAAGCAGTTAAGGAGATCAC
ACTGGAAAACAAGGACAGTGTAAAACTTCAAGATTGCTCAGCACTATGTGAAGAGGAAGAAAAGGAAGATGAAGGAGAAG
CTGCAGATATGGAAGAATATGAAGAGAGTGGATTGTTGGAAGCAGATGAGGCTACCCTAGATACAAGGAAAATAGTAGAA
GCTTGTAAAGCCAAAACTGATGCTGGCGATGAAGATGCTATTTTGCAAACCAGAATTTACGACCTTTACATCACTTATGA
TAAATATTACCAGACTCCACGATTATGGTTGTTTGGCTATGATGAGCAACTGCAGCCTTTAACAGTTGAGCACATGTATG
AAGACATCAGTCAAGATCATGTGAAGAAAACAGGGACCATTGAAAATCCCTCTCATCTACCACCACCTCCCATGTGTTCA
GTTCACCCATGCGGGCATGCTGAGGTGATGAAGAAAATAGTTGAGACTGTTGCAGATGGAGGGGGAGAACTTGGAGTTCA
TATGTATCTTCTTATTTTCTTGAAATTTGTACAAGCTGTCATTCCGACAATAGAA

Alignment

ORF - retro_nleu_331 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 90.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLPTGKQFLVTKNVPCYKRCKQMEY
          P......FKETGVITPEEFVAAG...VHHCPTWQWATGEELKVK.YLPTGKQFLVTKNV.CYK.CKQMEY
Retrocopy PRSSRNQFKETGVITPEEFVAAGNNIVHHCPTWQWATGEELKVKGYLPTGKQFLVTKNVLCYKPCKQMEY

Parental  SDELEAIIEEDDGDGGWVDTYHNTGITGITEAVKEITLENKDNIRLQDCSALCEEEEDEDEGEAADMEEY
          S.ELEAIIEE.DGDGGWVDT.HNT.ITGITEAVKEITLENKD...LQDCSALCEEEE.EDEGEAADMEEY
Retrocopy SEELEAIIEEEDGDGGWVDTHHNTSITGITEAVKEITLENKDSVKLQDCSALCEEEEKEDEGEAADMEEY

Parental  EESGLLETDEATLDTRKIVEACKAKTDAGGEDAILQTRTYDLYITYDKYYQTPRLWLFGYDEQRQPLTVE
          EESGLLE.DEATLDTRKIVEACKAKTDAG.EDAILQTR.YDLYITYDKYYQTPRLWLFGYDEQ.QPLTVE
Retrocopy EESGLLEADEATLDTRKIVEACKAKTDAGDEDAILQTRIYDLYITYDKYYQTPRLWLFGYDEQLQPLTVE

Parental  HMYEDISQDHVKKTVTIENHPHLPPPPMCSVHPCRHAEVMKKIIETVAEGGGELGVHMYLLIFLKFVQAV
          HMYEDISQDHVKKT.TIEN..HLPPPPMCSVHPC.HAEVMKKI.ETVA.GGGELGVHMYLLIFLKFVQAV
Retrocopy HMYEDISQDHVKKTGTIENPSHLPPPPMCSVHPCGHAEVMKKIVETVADGGGELGVHMYLLIFLKFVQAV

Parental  IPTIE
          IPTIE
Retrocopy IPTIE

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_331 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,