RetrogeneDB ID: retro_pvam_675

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_65:196730..197160(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP1
• Ensembl ID: ENSPVAG00000017876
• Aliases: None
• Description: nipsnap homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:7827]

Sequence

>retro_pvam_675
TTCTCAGGTGGCTACTCAGCCCTCAAGGACTGCATGAACAAGCTCTAAACAATGAGGAGTACCTGGAGTTCCTAAAGGAG
TGGAGCTAGATACTGCTGTCTGGGAAAAACCAGACCCTCCTCGAGGTGACTTCTGGAATGAGCCACAGCCCAGAGCAGGC
CCCACAATCTATGAGCTAAGGACATACCAGCTCACTCCAGGAACCATAATCAAGTGCGAGAACAACTGGTCTCAGGCCAT
CAAGTACCGACAGGAGAATCAGGAGGCAGTGGGCGGCTTCTTCTGGCAGACAGTGGGGCTCTACATTGTGTACCATCTCT
GGACCTATAAAGACCTGCAGCCTCAGGAGGAGACTAGAAATGCTACCTGGAGGAAGAGGGGTTTGGATGAAAATGTCTAC
TACACAGTTCCCTTGGTGCAACACATGGAG

Alignment

ORF - retro_pvam_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.97 %
• Parental protein coverage: 50.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSGGYPALMDCMNKL-KNNKEYLEFRKERSQMLLSRRNQMLLEFS-FWNEPQPRAGPNIYELRTYKLKPG
          FSGGY.AL.DCMNKL..NN.EYLEF.KE.S..LLS..NQ.LLE...FWNEPQPRAGP.IYELRTY.L.PG
Retrocopy FSGGYSALKDCMNKL<LNNEEYLEFLKEWS*ILLSGKNQTLLEVT<FWNEPQPRAGPTIYELRTYQLTPG

Parental  IMI--EGNNARAIKYRQENQEAVGGFFSQIGELYVVHHLWAYKDLQSREETRNAAWRKRGWDENVYYTVP
          ..I..E.N...AIKYRQENQEAVGGFF.Q...LY.V.HLW.YKDLQ..EETRNA.WRKRG.DENVYYTVP
Retrocopy TIIKCENNWSQAIKYRQENQEAVGGFFWQTVGLYIVYHLWTYKDLQPQEETRNATWRKRGLDENVYYTVP

Parental  LVRHME
          LV.HME
Retrocopy LVQHME

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_675 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012291	1 retrocopy	retro_cfam_2091,
Otolemur garnettii	ENSOGAG00000012167	1 retrocopy	retro_ogar_2741,
Pteropus vampyrus	ENSPVAG00000017876	1 retrocopy	retro_pvam_675 ,
Sus scrofa	ENSSSCG00000009988	1 retrocopy	retro_sscr_615,
Tupaia belangeri	ENSTBEG00000004614	3 retrocopies	retro_tbel_247, retro_tbel_4673, retro_tbel_968,