RetrogeneDB ID: retro_ptro_1434

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:36212046..36212804(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG3
• Ensembl ID: ENSPTRG00000015220
• Aliases: None
• Description: Autophagy-related protein 3 [Source:UniProtKB/TrEMBL;Acc:H2QN39]

Sequence

>retro_ptro_1434
TTGATTAATATGGTGAAGGAAAGGCATTAGAAGTAACTGAATACCTGACCTAATTCTCAAGGAATCAGTTTAAGGAAACA
GCTGTTATCACCCCAAAAGAGTTTATGGCAGCTGGAGATCACTTAGCTGTCCACTGCCCGACACAGCAATGGGCTACAGG
GAAAGAACTGAAAAGAGAGGCATAGCTACCAACAGGCAAATAATTTTTGGTAGCCAAAAATGTGGCATGCTACATCCAGT
CAAAACAGATGGCATATTCAGGTGAATTGGAAGCTATCACTGAAGATGATGGTGGTAGGGCATGGGTAGATACACATCAC
AGCACAGGAATTGCAGGAATAAACAAATAGGTTGAGGAGATTATACTTACAAGCAAAAATGGTATAAAACTCCAAAACTG
CTCAGCCTTATGAGAGGAAGAAGAAAAAGATGAAGGAAAATCTACATTTATGGAATAATATGAAGAGAGTGGGTTGCTGG
AAGCAGATAAAGCTACCCTAGATTAAAGGAAAATAGTAGAAGCTTGTAAAGCTTAAAGTGATGTTGGAGGTGAAGATGCT
CTTTTGCAAACCAAAACTTGTGACCTTTACATCACATATGGTAAATATTACCAGATGGCACAACTATGGTTTTTGGGCTA
TGACGAGGAACAGCAGATTTTCACAGCTGAATACAGGTATAAAGACATCATTCAAGACCATGTGAAGAAAACAGTGACCA
CTGAAAATCCCTCCACCAATCTCCCTCCACCTCCTATG

Alignment

ORF - retro_ptro_1434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.93 %
• Parental protein coverage: 81.21 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VINTVK-GKALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLPTGKQ
          .IN.VK.GKALEV.EYLT.......FKET.VITP.EF.AAGDHL..HCPT.QWATG.ELK..A.LPTGK.
Retrocopy LINMVK<GKALEVTEYLT*-FSRNQFKETAVITPKEFMAAGDHLAVHCPTQQWATGKELKREA*LPTGK*

Parental  FLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNTGITGITEAVKEITLENKDNIRLQDCSAL
          FLV.KNV.CY...KQM.YS.ELEAI.E.DDG...WVDT.H.TGI.GI...V.EI.L..K..I.LQ.CSAL
Retrocopy FLVAKNVACYIQSKQMAYSGELEAITE-DDGGRAWVDTHHSTGIAGINK*VEEIILTSKNGIKLQNCSAL

Parental  CEEEEDEDEGEAADMEEYEESGLLETDEATLDTRKIVEACKAKTDAGGEDAILQTRTYDLYITYDKYYQT
          .EEEE..DEG....ME.YEESGLLE.D.ATLD.RKIVEACKA..D.GGEDA.LQT.T.DLYITY.KYYQ.
Retrocopy *EEEE-KDEGKSTFME*YEESGLLEADKATLD*RKIVEACKA*SDVGGEDALLQTKTCDLYITYGKYYQM

Parental  PRLWLFGYDEQRQPLTVEHMYEDISQDHVKKTVTIEN-HPHLPPPPM
          ..LW..GYDE..Q..T.E..Y.DI.QDHVKKTVT.EN....LPPPPM
Retrocopy AQLWFLGYDEEQQIFTAEYRYKDIIQDHVKKTVTTENPSTNLPPPPM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	23.00 RPM
SRP007412_cerebellum	0.00 RPM	27.50 RPM
SRP007412_heart	0.00 RPM	25.91 RPM
SRP007412_kidney	0.00 RPM	33.40 RPM
SRP007412_liver	0.00 RPM	40.00 RPM
SRP007412_testis	0.00 RPM	110.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1434 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1434 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2479
Gorilla gorilla	retro_ggor_1544
Pongo abelii	retro_pabe_1827
Macaca mulatta	retro_mmul_594
Oryctolagus cuniculus	retro_ocun_1219
Equus caballus	retro_ecab_594

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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,