RetrogeneDB ID: retro_pabe_1827

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:36641715..36642473(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG3
• Ensembl ID: ENSPPYG00000013548
• Aliases: None
• Description: autophagy related 3 [Source:HGNC Symbol;Acc:20962]

Sequence

>retro_pabe_1827
TTGATTAATACAGTGAAAGAAAGGCACTAGAAGTAACTGAATACCTGACCTAATTCTCAAGGAATCAGTTTAAGGAAACA
GCTGTTATCACCCCAAAAGAGTTTATGGCAGCTGGAAATCACTTAGCTGTCCACTGCCCAACACAGCAACGGGTTATAGG
GGAAGAACTGAAAAGAGAGGCATAGCTACCAACAAGCAAATAATTTTTGGTAGCCAAAAATGTGGCATGCTACATCCAGT
CAAAACAGATGGCATATTCAGGTGAATTGGAAGCTGTCACTGAAGATGATGGTGGTAGGGCATGGGTAGATACACATCAC
AGCACAGGAATTGCAGGAATAAACAAATAGGTTGAGGAGATTATACTTACAAGCAAAAATGGTATAAAATTCCAAAACTG
CTCAACCTTATGAGAGGAAGAAGAAAAAGATGAAGGAAAATCTACATTTATGGAATAATATGAAGAGAGTGGGTTGCTGG
AAGCAGATAAAGCTACCCTAGACGAAAGGAAAATAGTAGAAGCTTGTAAAGCTTAAAGTGATGTTGGAGGTGAAGATGCT
CTTTTGCAAACCAAAACTTGTGACCTTTACATCATATATGGTAAATATTACCAGATGGCACAACTATGGTTCTTTGGCTA
TGATGAGGAACAGCAGATTTTCACAGATGAACACATGTATAAAGACATCATTCAAGACCATGTGAAGAAAACAGTGACCA
CTGAAAATCCCTCCACCAATCTCCCTCCACCTCCTATG

Alignment

ORF - retro_pabe_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.98 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VINTVKG-KALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLPTGKQ
          .INTVK..KALEV.EYLT.......FKET.VITP.EF.AAG.HL..HCPT.Q...GEELK..A.LPT.K.
Retrocopy LINTVKE<KALEVTEYLT*-FSRNQFKETAVITPKEFMAAGNHLAVHCPTQQRVIGEELKREA*LPTSK*

Parental  FLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNTGITGITEAVKEITLENKDNIRLQDCSTL
          FLV.KNV.CY...KQM.YS.ELEA..E.DDG...WVDT.H.TGI.GI...V.EI.L..K..I..Q.CSTL
Retrocopy FLVAKNVACYIQSKQMAYSGELEAVTE-DDGGRAWVDTHHSTGIAGINK*VEEIILTSKNGIKFQNCSTL

Parental  CEEEEDEDEGEAADMEEYEESGLLETDEATLDTRKIVEACKAKTDAGGEDAILQTRTYDLYITYDKYYQT
          .EEEE..DEG....ME.YEESGLLE.D.ATLD.RKIVEACKA..D.GGEDA.LQT.T.DLYI.Y.KYYQ.
Retrocopy *EEEE-KDEGKSTFME*YEESGLLEADKATLDERKIVEACKA*SDVGGEDALLQTKTCDLYIIYGKYYQM

Parental  PRLW-LGYDEQRQPLTVEHMYEDISQDHVKKTVTIEN-HPHLPPPPM
          ..LW..GYDE..Q..T.EHMY.DI.QDHVKKTVT.EN....LPPPPM
Retrocopy AQLWFFGYDEEQQIFTDEHMYKDIIQDHVKKTVTTENPSTNLPPPPM

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	0.00 RPM	29.03 RPM
SRP007412_cerebellum	0.00 RPM	23.10 RPM
SRP007412_heart	0.00 RPM	14.75 RPM
SRP007412_kidney	0.00 RPM	25.13 RPM
SRP007412_liver	0.00 RPM	21.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1827 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1827 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2479
Pan troglodytes	retro_ptro_1434
Gorilla gorilla	retro_ggor_1544
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,