RetrogeneDB ID: retro_pvam_1080

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_27230:5677..6146(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSPVAG00000014020
• Aliases: None
• Description: ATPase family, AAA domain containing 1 [Source:HGNC Symbol;Acc:25903]

Sequence

>retro_pvam_1080
TCAAATTGTGACCATAAAGCTACGGCCATGATGAAAGCTCAGTTTTGTGAGTCTCTGAGATGGATGGGATACTGACCACA
GCTGCGAGATCATAGTGAGGGGAGCTACTGATCATCCTCAGAATCTCGACCCAATTGTACTGATGAGAATGCCTGCAGGG
TTTCGTACCAACCAGCCTGCTCTTAAAGAAAGAAAAGCAATCCTGAAACTCATTTTGAAAAATGAAAATGTAGATAGACA
TGTGGACCTGCTAGAAGTTGCCCAGGAAACTGATGGGTTTTCAGGAAATGACCTAAAAGAAATGTGTTGAGATGCTGCCC
TCCTCTGTGTCAGAGAATATGTAAATTCTACATTAGAAGAAGGCCATAATGAAGATGAAATTTGGCCTGTGCAGCAACAG
GACCTGCATCGGGCAATTGAAAAGATGTAGTGAAAGGATGCAGCATTTCAGAATGTCTTAACACGTTTG

Alignment

ORF - retro_pvam_1080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 51.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSSDHEAPAMMKAQF-MSLWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILK
          S..DH.A.AMMKAQF..SL.DG.DTDHSC..IV.GAT..PQ.LD.....RMP..F..NQPALK.R.AILK
Retrocopy SNCDHKATAMMKAQF>VSL*DGWDTDHSCEIIVRGATDHPQNLDPIVLMRMPAGFRTNQPALKERKAILK

Parental  LILKNENVDRHVDLLEVAQETDGFSGSDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLQRAI
          LILKNENVDRHVDLLEVAQETDGFSG.DLKEMC.DAALLCVREYVNST.EE.H.EDEI.PVQQQDL.RAI
Retrocopy LILKNENVDRHVDLLEVAQETDGFSGNDLKEMC*DAALLCVREYVNSTLEEGHNEDEIWPVQQQDLHRAI

Parental  EKMKKSKDAAFQNVLTHV
          EKM.....A.FQNVLT..
Retrocopy EKM**KDAA-FQNVLTRL

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_1080 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080 ,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309,