RetrogeneDB ID: retro_pvam_394

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_292:126090..126758(+)
• Located in intron of: ENSPVAG00000012674

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSPVAG00000004662
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_pvam_394
TTTGTGAGAGCCTATGTCTTCATCACTTATGATGACTACAACCACTTCTTTGAAGATGTGTACACTCTCATTCCTGCTGT
AGCGATCATAGCTGTAGGAACCCTACTTTTCATTATTGGGCTAATTGGCTGCTGTGCCACAATCCACGAAAGCTGCTGTG
GACTGGCCACGTTTGTCATCATCCAACCCTGGGTTTTTGTCACAGAAGTCATTGTAATGGTTTTGGGATACATATATACA
GCAAAGGTGGAAAATGAGGTTGACCACAGCATTCAGAAAGTATGTAAGACCTACAATGAAACCAACCTTGATGCCGCTAG
CCAGGCTATAGATTATATATAGAGACAGCTGCACTGTTGTGGAATTCACAGCTACTCAGACTGGGAAAATACTGACTGGT
TCAAAGAAACCAAAAACCAGAGTGTCCCTCTCAGCTGCTGTAGAGAGACCTCCAGCAGCTGTTATGGTAGTCTGGCCTAT
CCCTCCAACCTCGCTCTGAGGGGTATGAGGCTCTAGTTGTGAAGAAGCTACAAGAAATCATGATGCATGTTATCTGGGCA
GCGCTGGCATTTGCAGCTCTTCAGCTGCTGGGCATGCTGTGTGCATGCATTGTGTTGCGCAGATAGAACAGAGATCTTAC
TTACAAGCTCCTCATCACTGGCAGAACC

Alignment

ORF - retro_pvam_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 88.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YVGAYVFITYDDYDHFFEDVYTLIPAVVIIAVGALLFIIGLIGCCATIRESHCGLATFVIILLLVFVTEV
          .V.AYVFITYDDY.HFFEDVYTLIPAV.IIAVG.LLFIIGLIGCCATI.ES.CGLATFVII...VFVTEV
Retrocopy FVRAYVFITYDDYNHFFEDVYTLIPAVAIIAVGTLLFIIGLIGCCATIHESCCGLATFVIIQPWVFVTEV

Parental  VVVVLGYVYRAKVENEVDRSIQKVYKTYNGTNPDAASRAIDYVQRQLHCCGIHNYSDWENTDWFKETKNQ
          .V.VLGY.Y.AKVENEVD.SIQKV.KTYN.TN.DAAS.AIDY..RQLHCCGIH.YSDWENTDWFKETKNQ
Retrocopy IVMVLGYIYTAKVENEVDHSIQKVCKTYNETNLDAASQAIDYI*RQLHCCGIHSYSDWENTDWFKETKNQ

Parental  SVPLSCCRETTSSCNGSLAYPSNL-YAEGCEALVVKKLQEIMMHIIWAALAFAAIQLLGMLCACIVLCRR
          SVPLSCCRET.SSC.GSLAYPSNL...EG.EALVVKKLQEIMMH.IWAALAFAA.QLLGMLCACIVL.R.
Retrocopy SVPLSCCRETSSSCYGSLAYPSNL<RSEGYEALVVKKLQEIMMHVIWAALAFAALQLLGMLCACIVLRR*

Parental  SRDPAYELLITGGT
          .RD..Y.LLITG.T
Retrocopy NRDLTYKLLITGRT

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_394 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394 ,
Pteropus vampyrus	ENSPVAG00000013681	1 retrocopy	retro_pvam_135,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,