RetrogeneDB ID: retro_pvam_91

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1309:158587..158941(+)
• Located in intron of: ENSPVAG00000012177

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2G
• Ensembl ID: ENSPVAG00000003481
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide G [Source:HGNC Symbol;Acc:9194]

Sequence

>retro_pvam_91
GGCAAGTATGGTTTTGCAATTGTTGTCACCACCATCGACAATGTCGGTACTGGTGTGATCCAGCCAGGCCAAGGCCTTGT
CCTTTATCCAGTTAAGTACAAGGCCATTGTTTTCCAGCCCTTTAAAGGGGAAGTCACAGATGTTGTTGTCACTCAGGTCA
GTAAGGTTGGACTCTTCACAGATATTGGACCTATGTCCTGCTTCATCTCTCAACACTGCATCCCATCAGAGATGGAGTTC
GAGCCTAACTCCAACCTACCATGTTGTTACAAGACAATTGATGAGGATATTGTGATTTAGCAGGATGATAAGATCTGCTT
GAAGATTGTGGGGACCTATGTGGATAAGAACGAT

Alignment

ORF - retro_pvam_91 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.36 %
• Parental protein coverage: 67.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIG-MSCFIS
          GKYGF.I.VTTIDN.G.GVIQPG.G.VLYPVKYKAIVF.PFKGEV.D.VVTQV.KVGLFT.IG.MSCFIS
Retrocopy GKYGFAIVVTTIDNVGTGVIQPGQGLVLYPVKYKAIVFQPFKGEVTDVVVTQVSKVGLFTDIGPMSCFIS

Parental  RHSIPSEMEFDPNSN-PPCYKTMDEDIVIQQDDEIRLKIVGTRVDKND
          .H.IPSEMEF.PNSN.P.CYKT.DEDIVI.QDD.I.LKIVGT.VDKND
Retrocopy QHCIPSEMEFEPNSNLPCCYKTIDEDIVI*QDDKICLKIVGTYVDKND

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_91 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018688	1 retrocopy	retro_cjac_641,
Dipodomys ordii	ENSDORG00000015696	1 retrocopy	retro_dord_574,
Macropus eugenii	ENSMEUG00000011547	1 retrocopy	retro_meug_139,
Myotis lucifugus	ENSMLUG00000011039	1 retrocopy	retro_mluc_261,
Pteropus vampyrus	ENSPVAG00000003481	1 retrocopy	retro_pvam_91 ,