RetrogeneDB ID: retro_pvam_235

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2060:319516..320211(-)
• 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_235
GCGGGCACCCTGCTCACTCCCATCCCGGTGGAGGGCTCTCCACAGCCAAATCTACCAGCAGGGGAGCAGCTGGAGGGTGC
TAATCAGGCCCAGGGCTCAGATCCCTGCCTTTCTACCCTTGGCATTGCACTGACACCTATGAAGACAAGCAGCAGAGAGC
CCCCAAGCCCACTGGTGAAACAGCTGAATGAAGTATTTAAGACTGAAGCCCCCAAATCGAACCTTCCCCAGAGCCTGTTC
TTCCCCTAGAGGTGCCTTCATCTTCTGAATTGGACTTGCCTCTAAGCACCCAGTTTTCCCTCGAGGACCAGATGCCTCAT
TGGAGTCAGACTGAGCTCCCTTCCAAGCAGGTGTATTTCAAGGAGGAAACAGGAACGCCTATGGCCAGGTGGGGCTCAAA
CAAGCCCTTGAGAGACCCAGTTAGGGCCAGATCTTCAGGTTCTAAGTGCAACAGACGGAAACCAAACAGCAAGGTACTAG
GGAGCTCTCCCCTCACCACCCTGCAGGATGACAACTCCCTCCCCTAGACTCTGACACCAGGACAGGGTAAGCAACCTTCT
CCTCTAGGTGAAAATGGTAGGGAACTAAAGGAAGGGGCCATTCTGGGAACTGGATGACTTCTGAGAACTGGACGAGTATG
AGAGCAAGGCCAAGACTATGACAAGGAAAACCAGCACTTTGTCTTGATAGAGAAC

Alignment

ORF - retro_pvam_235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.69 %
• Parental protein coverage: 88.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGILRTPIQVESSPQPNLPARDQLEGSNQAQGSDPRSPTLGIART-MKTSSGEPPSPLVKELSEVFETEG
          AG.L.TPI.VE.SPQPNLPA..QLEG.NQAQGSDP...TLGIA.T.MKTSS.EPPSPLVK.L.EVF.TE.
Retrocopy AGTLLTPIPVEGSPQPNLPAGEQLEGANQAQGSDPCLSTLGIALTPMKTSSREPPSPLVKQLNEVFKTEA

Parental  PKSNLP-PETVLPLEAPSSSELDLPVGTQFSLEDKMAPGSQTELPSKQVFSEEETGQPSETPMASQSSDK
          PKSNLP.PE.VLPLE.PSSSELDLP..TQFSLED.M...SQTELPSKQV...EETG....TPMA...S.K
Retrocopy PKSNLP<PEPVLPLEVPSSSELDLPLSTQFSLEDQMPHWSQTELPSKQVYFKEETG----TPMARWGSNK

Parental  PLRDLETPRSSGSKRSRRKPNGKVLGRSPLTILQDDNS-PGTLA-RQVKRLSPLSENVRELKEGTILGTG
          PLRD....RSSGSK..RRKPN.KVLG.SPLT.LQDDNS.P.TL...Q.K..SPL.EN.RELKEG.ILGTG
Retrocopy PLRDPVRARSSGSKCNRRKPNSKVLGSSPLTTLQDDNSLP*TLTPGQGKQPSPLGENGRELKEGAILGTG

Parental  RLLRTGGQTWEQGQDHDKENQHFALVEN
          .LLRT.G...EQGQD.DKENQHF.L.EN
Retrocopy *LLRT-GRV*EQGQDYDKENQHFVLIEN

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_235 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,