RetrogeneDB ID: retro_pvam_940

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_1795:94031..94547(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIDA
• Ensembl ID: ENSPVAG00000010662
• Aliases: None
• Description: axin interactor, dorsalization associated [Source:HGNC Symbol;Acc:25761]

Sequence

>retro_pvam_940
GAAGAAGATGAGGAAGAGGGTGGTGCTGGAGTAGGGTCTCCTGGTTTCTCTCCTGCTAGAGTTCTTGGTACATTATTACC
AAGGTTGTCATCAGAGCCAGGAATAATGTTATTCACTATCAGAATTAAGAACGTTGGTCTGAAAGATGCTGGGCAGTGCA
TTGATCCCTATATCACAGTTGGTGTAAAGGATCTGAATGGCATAAATTTAACTCCTGTGCAAGATACTCCTGTGGCTTCA
AGAAAAGAAGATACATATGCTTATTTTAATGTGGAAATTAATTCCCAGAGGTAGTCTGTAAAATTAACAAAAGTTGCAGC
TATCTTCTTTGAATTCAAATGCTACAAGCTTAAAAAAGGTTTACCAGTACAAAGTGTTGCTTTCATGGAAATGGATGAAA
TTAAACCTGAGCTAATTGTAGCAGAACTATACAAGAAACCCACTGACTTTAAAAGAAGGAAATTAAAATTATTGACCAAG
AAACCACTTTATCTATATCAAACTTTGCACAAGGAA

Alignment

ORF - retro_pvam_940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 57.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEDEEEGGAGAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDL
          EEDEEEGGAG.GSP...PARV.GTLLPRL.SEPG..L.TIRI...GLKDAGQCIDPYITV.VKDLNGI.L
Retrocopy EEDEEEGGAGVGSPGFSPARVLGTLLPRLSSEPGIMLFTIRIKNVGLKDAGQCIDPYITVGVKDLNGINL

Parental  TPVQDTPVASRKEDTYVHFNVDIELQKHVEKLTKGAAVFFEFKHYKPKKRFTSTKCFAFMEMDELRPGPI
          TPVQDTPVASRKEDTY..FNV.I..Q....KLTK.AA.FFEFK.YK.KK........AFMEMDE..P..I
Retrocopy TPVQDTPVASRKEDTYAYFNVEINSQR*SVKLTKVAAIFFEFKCYKLKKGLP-VQSVAFMEMDEIKPELI

Parental  VIELYKKPTDFKRKKLQLLTKKPLYLHLHQTLHKE
          V.ELYKKPTDFKR.KL.LLTKKPLY..L.QTLHKE
Retrocopy VAELYKKPTDFKRRKLKLLTKKPLY--LYQTLHKE

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_940 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448,
Mus musculus	ENSMUSG00000042901	3 retrocopies	retro_mmus_1939, retro_mmus_3098, retro_mmus_763,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688,
Pteropus vampyrus	ENSPVAG00000010662	1 retrocopy	retro_pvam_940 ,