RetrogeneDB ID: retro_pvam_153

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1668:98664..99381(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSPVAG00000008017
• Aliases: None
• Description: primase, DNA, polypeptide 1 (49kDa) [Source:HGNC Symbol;Acc:9369]

Sequence

>retro_pvam_153
GGAGTCATAAAGAATTACTTTAAACACCGTGAATTTAATTCACATTGAAAGATGATATTTACATTTGCTACCTAATCCTT
CTACAGCCCGAGTGATCTGGAAAAAGAGATGCAAAAAATAAATCCGACGAGATTAATATAGGCACGGTATATTCCCACAG
ACCCAATCAACACAATACGATGAAGCTGGAAGCTTTCTAGGCTCAAGAAAAAGACCTGGTGTTTGACATTGACATAGCCG
ACTGTGACTGCCTGAGGCGATGTTACAGTTCTACAGACACATGTACTAAATGCTGGATCCTCATGACAGTGCCCATTCTC
ATCATCAATTGACCATTGAAGAAGGACTTTGGATTTAAGCTTCGTCTCTGAGTGTTTTCGGGAAGGAGAGGTGTTTATTT
GCTGGATCCGTGATGAATCATAAAACTGTCCTCTGCAGCACATTCTGGGATAATTGAGTGTTTGAATCTTGTAAAGTGTG
GTTAAGAGGTAAAAAGAAAGTTTACCTAAGTGAAAAAAATCCACCCTTTATCAGAAAACCTGTAAACATAATTAAAAAGT
ACTTTGAGGAATATGCGTTGATTGATCAAGATATTCTTGAAAATAAAGAAAACCGCGGTAAGATTTTAGCCCTTGTTCCT
GAAACAATTCATGGTGAACGCAACCAAACTTCCAAAAGCTTCACAGTTCACTTCAGCGTTTGAAGCATTTGAAGAAG

Alignment

ORF - retro_pvam_153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.9 %
• Parental protein coverage: 57.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GVIKNYFQHREFS-FTLKDDIYIRYQ-SFNNQSDLEKEMQKMNPYK-IDIGAVYSHRPNQHNTVKLGAFQ
          GVIKNYF.HREF..FTLKDDIYI.Y..SF...SDLEKEMQK.NP...I.IG.VYSHRPNQHNT.KL.AF.
Retrocopy GVIKNYFKHREFN<FTLKDDIYICYL>SFYSPSDLEKEMQKINPTR<INIGTVYSHRPNQHNTMKLEAF*

Parental  AQEKELVFDIDMTDYDDVRRCCSSADICSKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVH-CWV
          AQEK.LVFDID..D.D..RRC.SS.D.C.KCW.LMT..I.II...LK.DFGFK.RL.V.SGRRGV..CW.
Retrocopy AQEKDLVFDIDIADCDCLRRCYSSTDTCTKCWILMTVPILIIN*PLKKDFGFKLRL*VFSGRRGVY>CWI

Parental  CDES-VRKLSSAVRSGIVEYLSLVKGGPDV-KKKVHLSEKIHPFVRKSINIINKYFEEYALVDQDIXXXX
          .DES.....S.A..SGI.E.L.LVK.G..V.KKKV.LSEK..PF.RK..NII.KYFEEYAL.DQDI....
Retrocopy RDES<IKLSSAA-HSGIIECLNLVKCG*EV<KKKVYLSEKNPPFIRKPVNIIKKYFEEYALIDQDILENK

Parental  XXXXXXXXXXXXXIHDE-LQQSFQNHHSSLQRWEHLKK
          .............IH.E..Q..FQ..HSSLQR..HLKK
Retrocopy ENRGKILALVPETIHGE<TQPNFQKLHSSLQRLKHLKK

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_153 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153 , retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,