RetrogeneDB ID: retro_pvam_19

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3244:19360..19879(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000000698
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CETN3
• Ensembl ID: ENSPVAG00000017925
• Aliases: None
• Description: centrin, EF-hand protein, 3 [Source:HGNC Symbol;Acc:1868]

Sequence

>retro_pvam_19
ATGGCTTCCAGCTTTAAGAAGCCAAACGTGCCCTCTACCAGCCAAAAGAGAAAGGTGGGTCCTAAGCCTGAACTCACTGA
AGATCAGAAGCAAGAAGTTCGCGAAGCGTTTGACCTCTTCGATGCTGACGGAAGTGGGACCATCGACGTGAAGGAGCTGA
AGGTGGCTATGAGAGCGCTGGGCTTTGAACCCAGAAAGGAAGAGATGAAGAAGATGATCTCCGAGGTGGACAAGGAAGGT
ACGGGGAAAATTAGCTTCAATGATTTCTTGGCTGTGATGACTCAGAAGATGGCCGAGAAAGACACCAAAGAAGAGATTCT
AAAGGCTTTCAGGCTCTTCGATGATGATGAAACTGGGAAGATCTCTTTCAAAAACCTGAAGCGTGTGTCCCACGAGTTGG
GGGAAAACCTCACTGATGAGGAGCTGCAGGAAATGATTGACGAAGCCGATCGGGATGGAGACGGCGAAGTGAACGAAGAA
GAGTTTCTTCGCATCATGAAAAAGACCAACCTCTATTAA

Alignment

ORF - retro_pvam_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.62 %
• Parental protein coverage: 90.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTKRKKRRELSEEQKQEIKDAFELFDTDKDEAIDYHELKVAMRALGFDVKKADVLKILKDYDREATGKIT
          K.K.....EL.E.QKQE...AF.LFD.D....ID..ELKVAMRALGF...K....K.....D.E.TGKI.
Retrocopy KRKVGPKPELTEDQKQEVREAFDLFDADGSGTIDVKELKVAMRALGFEPRKEEMKKMISEVDKEGTGKIS

Parental  FEDFNEVVTDWILERDPHEEILKAFKLFDDDDSGKISLRNLRRVARELGENMSDEELRAMIEEFDKDGDG
          F.DF..V.T....E.D..EEILKAF.LFDDD..GKIS..NL.RV..ELGEN..DEEL..MI.E.D.DGDG
Retrocopy FNDFLAVMTQKMAEKDTKEEILKAFRLFDDDETGKISFKNLKRVSHELGENLTDEELQEMIDEADRDGDG

Parental  EINQEEFIAIM
          E.N.EEF..IM
Retrocopy EVNEEEFLRIM

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_19 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007233	1 retrocopy	retro_dord_30,
Otolemur garnettii	ENSOGAG00000002383	1 retrocopy	retro_ogar_3511,
Ochotona princeps	ENSOPRG00000002381	1 retrocopy	retro_opri_17,
Procavia capensis	ENSPCAG00000006854	1 retrocopy	retro_pcap_403,
Pteropus vampyrus	ENSPVAG00000017925	1 retrocopy	retro_pvam_19 ,
Tupaia belangeri	ENSTBEG00000001992	2 retrocopies	retro_tbel_4470, retro_tbel_4732,