RetrogeneDB ID: retro_pvam_297

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2407:219268..219724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA3
• Ensembl ID: ENSPVAG00000012300
• Aliases: None
• Description: cell division cycle associated 3 [Source:HGNC Symbol;Acc:14624]

Sequence

>retro_pvam_297
ATGGACTTCACCAAGAGCGTCCCAGCCACTCCAGCGTGAGCTCGGAGCACAGCAAGCATCTGGCTTGAGGGGCGCCCCAC
GCTCACCTAGTGCGGGCATCATGCACACCCCCGTGCAGGTGGAGAGCTTTCTACAGCCAAACCTGCCAGCAGGGGGCAGC
TGGAGGGTCCCAATCAGGCCTGGGGCTCAGACCCCCACTCTCCTGCCCTTAGCATTGCAGACACCTGTGAAGACCAGCTG
TGGAGAGCCTCCAAGCCCACGGGTGAAACAGCTGAGTGAAGTATTTGAGATCGAAGCCCCCAGATCAAACCTCCCCCCAG
AGCCTGTTCTGCCCCTAGAGGCCCTTTGTCTTCTGAATTGGACTTGCCTCTGGGCACCCAGTTTTCCCTGGAGGACCAGA
TGCCACCTTGGAGTCAGATTGAGCAGGTGTTTTCCAAAGAGGAAACAGGACAGCCA

Alignment

ORF - retro_pvam_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.75 %
• Parental protein coverage: 59.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGSAKSVPVTP-SRPPPRNKHLARVAD-PRSPSAGILRTPIQVESSPQPNLPA-RDQLEGSNQAQGSDPR
          M...KSVP.TP.S......KHLA..A..PRSPSAGI..TP.QVES..QPNLPA.R.QLEG.NQA.GSDP.
Retrocopy MDFTKSVPATP<SVSSEHSKHLA*GAP<PRSPSAGIMHTPVQVESFLQPNLPA<RGQLEGPNQAWGSDPH

Parental  SPTLGIART-MKTSSGEPPSPLVKELSEVFETEGPKSNLPPETVLPLEA-PSSSELDLPVGTQFSLEDKM
          SP.L.IA.T..KTS.GEPPSP.VK.LSEVFE.E.P.SNLPPE.VLPLEA.P.SSELDLP.GTQFSLED.M
Retrocopy SPALSIADT>VKTSCGEPPSPRVKQLSEVFEIEAPRSNLPPEPVLPLEA<PLSSELDLPLGTQFSLEDQM

Parental  APGSQTELPSKQVFSEEETGQP
          .P.SQ.E....QVFS.EETGQP
Retrocopy PPWSQIE----QVFSKEETGQP

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_297 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013985	1 retrocopy	retro_amel_1158,
Canis familiaris	ENSCAFG00000014650	4 retrocopies	retro_cfam_1100, retro_cfam_1940, retro_cfam_345, retro_cfam_633,
Cavia porcellus	ENSCPOG00000012334	1 retrocopy	retro_cpor_1073,
Felis catus	ENSFCAG00000004274	2 retrocopies	retro_fcat_1182, retro_fcat_1942,
Mustela putorius furo	ENSMPUG00000016781	1 retrocopy	retro_mputfur_663,
Pteropus vampyrus	ENSPVAG00000012300	4 retrocopies	retro_pvam_235, retro_pvam_248, retro_pvam_297 , retro_pvam_667,
Rattus norvegicus	ENSRNOG00000015529	1 retrocopy	retro_rnor_2685,
Ictidomys tridecemlineatus	ENSSTOG00000023573	1 retrocopy	retro_itri_804,
Tupaia belangeri	ENSTBEG00000001905	1 retrocopy	retro_tbel_534,
Vicugna pacos	ENSVPAG00000009784	1 retrocopy	retro_vpac_296,