RetrogeneDB ID: retro_pvam_1399

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_79:136465..137018(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG3
• Ensembl ID: ENSPVAG00000009568
• Aliases: None
• Description: autophagy related 3 [Source:HGNC Symbol;Acc:20962]

Sequence

>retro_pvam_1399
GGGGAAGAATGAAAGCGAAGGCATACCTAGCAATAGCAAGAAATTTTTGCTAACCAAAAATGTGCCATGCTGGACATGGT
GCAAACAGGCGCAATAGTCATGTGATTTGTAAGTTCTCACTGAAGAAGATGACGATGACAGGAGATGGGGAGATACGTTG
TCACGACATAGGGACCTGCAAGAATAATCAAAGCAGTTAAAGTGATTACACTGGAAAGAAAAGACAGTATAAAACTCCAA
GTTTGCTCAGCATTCTGTGAGGAGGATGAAAAGAAAGATTTTAAAAAGCTGCAGCTCCGGAAGATTATGAAGAGAGTCGA
TTTTGGGGACCAGATGAGGCTATTCTAGCTGCAAGGAAAATAGTAGAGGCTCGTAAAGTGAAAACTGATATTGGAGGTGA
AGGTGATATTTTGCAAACCAGAACTTATGACCTCTACATAAGTTATAAATATTACCGGATGCCATAGCCATGGTCGTTAG
CTATGGTCAGCAAAGGCAGCCTTTAACGGTTGAGCACATGTATGAAAACATCAGTCAAGATTATGAGAAGAAA

Alignment

ORF - retro_pvam_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.38 %
• Parental protein coverage: 59.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GEE-LKVKAYLP-TGKQFLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTY-HNTGI-AGITEAV
          GEE..K.KAYL....K.FL.TKNVPC...CKQ...S..L....EEDD.D..W.DT..H..G..A.I..AV
Retrocopy GEE<MKAKAYLA<NSKKFLLTKNVPCWTWCKQAQ*SCDL*VLTEEDDDDRRWGDTL>HDIGT>ARIIKAV

Parental  KEITLESKDSVKLQDCSALCEEEEEEDEG-EAADMEEYEESGLLETDEATLDTRKIAEACKAKTDAGGED
          K.ITLE.KDS.KLQ.CSA.CEE.E..D....AA..E.YEES.....DEA.L..RKI.EA.K.KTD.GGE.
Retrocopy KVITLERKDSIKLQVCSAFCEEDEKKDFK<KAAAPEDYEESRFWGPDEAILAARKIVEARKVKTDIGGEG

Parental  AILQTRTYDLYITYDKYYQTPRLW-LFGYDEQRQPLTVEHMYEDISQDHVKK
          .ILQTRTYDLYI.Y.KYY..P..W....Y..QRQPLTVEHMYE.ISQD..KK
Retrocopy DILQTRTYDLYISY-KYYRMP*PW<VVSYGQQRQPLTVEHMYENISQDYEKK

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_1399 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 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 ,