RetrogeneDB ID: retro_pvam_574

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_386:171536..171855(-)
• Located in intron of: ENSPVAG00000005368

Retrocopy information

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

Parental gene information

• Parental gene symbol: HPCA
• Ensembl ID: ENSPVAG00000000363
• Aliases: None
• Description: hippocalcin [Source:HGNC Symbol;Acc:5144]

Sequence

>retro_pvam_574
GTCGCGCTGAGCGTCACCTCCCGCGGCAAGCTGGAGCAGAAGCTCAAGTGGGCCTTCAGCTTCTACGACCTGGATGGCAG
AGGCTACATCAGCCGCAGCGAGAGGATGGAGATCGTGCAGGCTATTTACAAAATGGTGTCCTCGGTGATAAAGATGCCAA
GGAGGAGTTCAGCCCGGAGAAATGGACAGACAAGATCTTCAGGCAGATGGACACCAACAATGAAGACAAACTGTCCCTGG
AGAATTTACTAAAGATGCCAAAAGTGACCCCTCCATCGTCCGGTTGTTACAGTGTGACCCCAGCAACGGAAGTCAGTTC

Alignment

ORF - retro_pvam_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.98 %
• Parental protein coverage: 55.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IALSVTSRGRLEQKLMWAFSMYDLDGNGYISREEMLEIVQAIYKMVSSVMKMP-EDESTPEKRTEKIFRQ
          .ALSVTSRG.LEQKL.WAFS.YDLDG.GYISR.E..EIVQAIYKMVSSV.KMP...E..PEK.T.KIFRQ
Retrocopy VALSVTSRGKLEQKLKWAFSFYDLDGRGYISRSERMEIVQAIYKMVSSVIKMP<KEEFSPEKWTDKIFRQ

Parental  MDTNNDGKLSLE-EFIRGAKSDPSIVRLLQCDPSSASQF
          MDTNN..KLSLE.EF...AKSDPSIVRLLQCDPS..SQF
Retrocopy MDTNNEDKLSLE<EFTKDAKSDPSIVRLLQCDPSNGSQF

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_574 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001865	1 retrocopy	retro_meug_4,
Pteropus vampyrus	ENSPVAG00000000363	1 retrocopy	retro_pvam_574 ,