RetrogeneDB ID: retro_pvam_544

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3665:255174..255489(-)
• Located in intron of: ENSPVAG00000014356

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDE6D
• Ensembl ID: ENSPVAG00000004743
• Aliases: None
• Description: phosphodiesterase 6D, cGMP-specific, rod, delta [Source:HGNC Symbol;Acc:8788]

Sequence

>retro_pvam_544
GAAGCCCGTGTTCCCAAGAAAATTCTCAAGTGCAAGGCAGTGTCTCGAGAATTGAACTTCTATCAGCAGAGCAAATGGAA
AAATTTTTACCAGGAACAAAAAGTTTACTTCAAAGGACAATGCCTAGAAGAATGGTTCTTCGAGTTTGGCTTTGTGATTC
CTAACTCCACAAGCACCTGGCAGTACCTGATGGAGGCGGCACTCGAGTCCCAGATGATGCCAGCCAGAGTGCTCACTGGG
AATGTTATCATAGAGACAAAGTTTTTTGATGACGATCTTCTTGTAAGCACATCCAGAGTGAGACTTTTCTACGTT

Alignment

ORF - retro_pvam_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.79 %
• Parental protein coverage: 74.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLRVPKKILKCKAVSRELNFS-SAEQMEKFR-LEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAP
          ..RVPKKILKCKAVSRELNF..SAEQMEKF...EQKVYFKGQCLEEWFFEFGFVIPNST.TWQ.L.EAA.
Retrocopy EARVPKKILKCKAVSRELNFY<SAEQMEKFL>QEQKVYFKGQCLEEWFFEFGFVIPNSTSTWQYLMEAAL

Parental  ESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
          ESQMMPA.VLTGNVIIETKFFDDDLLVSTSRVRLFYV
Retrocopy ESQMMPARVLTGNVIIETKFFDDDLLVSTSRVRLFYV

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_544 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
Anolis carolinensis	ENSACAG00000012101	1 retrocopy	retro_acar_157,
Dasypus novemcinctus	ENSDNOG00000000568	1 retrocopy	retro_dnov_2585,
Felis catus	ENSFCAG00000002232	1 retrocopy	retro_fcat_317,
Macropus eugenii	ENSMEUG00000006427	1 retrocopy	retro_meug_1355,
Oryctolagus cuniculus	ENSOCUG00000010403	1 retrocopy	retro_ocun_182,
Pteropus vampyrus	ENSPVAG00000004743	1 retrocopy	retro_pvam_544 ,
Tursiops truncatus	ENSTTRG00000009165	1 retrocopy	retro_ttru_82,