RetrogeneDB ID: retro_pvam_562

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3760:149726..150155(-)
• Located in intron of: ENSPVAG00000024205

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM106C
• Ensembl ID: ENSPVAG00000014352
• Aliases: None
• Description: transmembrane protein 106C [Source:HGNC Symbol;Acc:28775]

Sequence

>retro_pvam_562
TTCCTGTTTCCACATTCAGCCCATGTGGATGGTGATGGCATCAGAGTAGTCAAAGTTACATTTAATAAGCAGGAATCCCT
TGTAATCCTCGCCATCACGGTGACCCTGAGAATCAGGAACTCTAGCTTCTACTCTGTAGCAGTGACCAGCCTTTCCAGAC
ATGTTCAGTACATGAACACAGTGGTTGGGTCACATGTGACAACTACCATTTCCTTCTTTCCACCTCAGAGTGAGCAACTG
GTGAATTTTCCAGTGCAGGCTGGAGGAGCGTTTTCCTTTGTGTACTTTTGCACATTACCCGATATCCAGGTGCACAACAT
AGTGATCTTCATGAGAACTTTGGCGAAGATTTCATACATTGGCCACGTGACTCAGAGCTCCTTGGAGACACATCACTATG
TGGATTGTGGAGCAAATTACCTAGCTATT

Alignment

ORF - retro_pvam_562 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.08 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLFPHSVLVDDGGIRVVKVTFNKQDSLVILAIKATLKIRNSNFYPVAVTSLSSQVQYMNTVVGSYTTANV
          FLFPHS..VD..GIRVVKVTFNKQ.SLVILAI..TL.IRNS.FY.VAVTSLS..VQYMNTVVGS..T...
Retrocopy FLFPHSAHVDGDGIRVVKVTFNKQESLVILAITVTLRIRNSSFYSVAVTSLSRHVQYMNTVVGSHVTTTI

Parental  SLIPPRSEQLVNFMEQAEMGGPFSYVYFLCTLPDIQVHNIVIFMRTSVKISYIGHVTQSSLETHHYVDCG
          S..PP.SEQLVNF..QA..GG.FS.VYF.CTLPDIQVHNIVIFMRT..KISYIGHVTQSSLETHHYVDCG
Retrocopy SFFPPQSEQLVNFPVQA--GGAFSFVYF-CTLPDIQVHNIVIFMRTLAKISYIGHVTQSSLETHHYVDCG

Parental  ANSTAV
          AN..A.
Retrocopy ANYLAI

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_562 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008335	1 retrocopy	retro_cpor_1124,
Equus caballus	ENSECAG00000020351	1 retrocopy	retro_ecab_660,
Echinops telfairi	ENSETEG00000010370	1 retrocopy	retro_etel_173,
Myotis lucifugus	ENSMLUG00000017734	1 retrocopy	retro_mluc_1096,
Pteropus vampyrus	ENSPVAG00000014352	1 retrocopy	retro_pvam_562 ,
Sus scrofa	ENSSSCG00000028397	1 retrocopy	retro_sscr_473,
Tarsius syrichta	ENSTSYG00000001184	1 retrocopy	retro_tsyr_1263,