RetrogeneDB ID: retro_pvam_567

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_379:96456..96938(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA5
• Ensembl ID: ENSPVAG00000007908
• Aliases: None
• Description: cell division cycle associated 5 [Source:HGNC Symbol;Acc:14626]

Sequence

>retro_pvam_567
ATGTCCAAGAGGCGAACGCGGTCCGGAGGGCCTTCCCAGCGCCTGAGCCAGGGGCCCCGTCCTCTATTCAGTCTCTGCGG
ATGTCCCAGTGGAAATCAGGCTCTGATCTCCCCAGCACCTTCCCTGAAATCTGGCCAAAGGCACCCCATGCAGCTCCACT
CAGAAAGCCCATCGTCCTGAAGAAGATCGTAGCCCATGCTGTAAAGATCCCATCTGTCCACTCGCCTCCAAGGAGCCCTA
GGATCGCCTTTTTCTTGGAGAAAGAAAACGAGCCTCCTCGCCAGGAACCTACTGGGGAGGACCTCTTCAAGACATGTAGT
GTCCCTGTCACCCCCACCACCACTCCTGTGATATATGACCTAGATGTTGAGTCTAGCTCCAGGGGACGAGACCTAGACAC
CAGAGACTTGGAAATGTCTAAGAAAGTCAGGCGCTCCTACAGCGGGCTGGAGCCCCTTGGCTGTGCCTCTCCACCTCCAC
CC

Alignment

ORF - retro_pvam_567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 71.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSERRTRSGGAAQR-PEPAAPSSTQSLRRSQRKSGSDLPSTLPEIWPKAPLAAPVRKPIVLKKIVAHAVK
          MS.RRTRSGG..QR.PEP.APSS.QSLR.SQ.KSGSDLPST.PEIWPKAP.AAP.RKPIVLKKIVAHAVK
Retrocopy MSKRRTRSGGPSQR<PEPGAPSSIQSLRMSQWKSGSDLPSTFPEIWPKAPHAAPLRKPIVLKKIVAHAVK

Parental  IPSVHSPRRSPRIAFFLEKENKPPGQEPTREDLFKSCSVPSTPTTTPVLCNPDVESNSREQDLDTRDLEM
          IPSVHSP.RSPRIAFFLEKEN.PP.QEPT.EDLFK.CSVP.TPTTTPV....DVES.SR..DLDTRDLEM
Retrocopy IPSVHSPPRSPRIAFFLEKENEPPRQEPTGEDLFKTCSVPVTPTTTPVIYDLDVESSSRGRDLDTRDLEM

Parental  SKKVRRSYSRLETLGCASTSTP
          SKKVRRSYS.LE.LGCAS...P
Retrocopy SKKVRRSYSGLEPLGCASPPPP

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_567 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002502	1 retrocopy	retro_cjac_4145,
Dasypus novemcinctus	ENSDNOG00000019033	1 retrocopy	retro_dnov_2601,
Felis catus	ENSFCAG00000028197	1 retrocopy	retro_fcat_761,
Pteropus vampyrus	ENSPVAG00000007908	1 retrocopy	retro_pvam_567 ,
Rattus norvegicus	ENSRNOG00000046635	2 retrocopies	retro_rnor_639, retro_rnor_640,