RetrogeneDB ID: retro_pvam_156

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1674:127327..127610(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM13
• Ensembl ID: ENSPVAG00000000073
• Aliases: None
• Description: translocase of inner mitochondrial membrane 13 homolog (yeast) [Source:HGNC Symbol;Acc:11816]

Sequence

>retro_pvam_156
GAAGGCAGCTTTGGCTTGGATTTCGGGGGCTCCAGTGGTGTCAGTCTGGACTCCAGGGATCATCATGGAGCAGGTGAAAG
GTACAGATCGCTATAGCCAACGCTCTGGAGCTTCGCAGAGAATGATGGACAAGTGCTTCCAGAAGTGCATTGGGAAGCCG
GTGGGCTCTCTGGATAATTCAAAGCAGAAGTGCATCGCCATGTACATGGATCAGTGCATGGATGCCTGGAACACCGTGTC
CTGCACTTACAACTCTTGGCTGCAGTGGGAATGAGCCAACATG

Alignment

ORF - retro_pvam_156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.29 %
• Parental protein coverage: 98.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EGGFGSDFGGSSGGKLD-PGLIMEQVK-VQIAVANAQELL-QRMTDKCFRKCIGKPGGSLDNSEQKCIAM
          EG.FG.DFGGSSG..LD.PG.IMEQVK.VQIA.ANA.EL..QRM.DKCF.KCIGKP.GSLDNS.QKCIAM
Retrocopy EGSFGLDFGGSSGVSLD>PGIIMEQVK>VQIAIANALELR<QRMMDKCFQKCIGKPVGSLDNSKQKCIAM

Parental  CMDRYMDAWNTVSRAYNSRLQRERANM
          .MD..MDAWNTVS..YNS.LQ.E.ANM
Retrocopy YMDQCMDAWNTVSCTYNSWLQWE*ANM

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_156 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016259	2 retrocopies	retro_etel_1313, retro_etel_49,
Otolemur garnettii	ENSOGAG00000013643	1 retrocopy	retro_ogar_1157,
Pteropus vampyrus	ENSPVAG00000000073	1 retrocopy	retro_pvam_156 ,