RetrogeneDB ID: retro_pvam_294

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2385:339989..340493(-)
• Located in intron of: ENSPVAG00000000170

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSPVAG00000006297
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_pvam_294
CAGAATAGAAAAAGTAGAAGAGTTGAAACAGCAGAGCCTGAAGAATTTGTGGTCGAAGAAGTACTAGACCAAAGCGTACT
GAATGGGAAAGTGGAGTACTTCCTAAAGTGGACGGGATTCACAGATGCCGACAATACTTGGGAACTGGAAGAAAATTTAG
ATAATCCAGAGTTAAGTGAAGCATTTCTTAATTCTCAAAAAGCTGGTAAAGAAAAAGATGGTACAAAAAGAGAAACTTTA
TCTGGCAATGAGTCTGATGATAGCAAATCAAAGAAGAAAAGAGATGCTGCTGATTAACCAAGAGGTTTTGCCAGAGGCCT
TGATCCTGAATGAGTAATTGGTGCCACAGACAACAATGGAGAATTAATGTTTCTCATAAAATGGAAAGATTACGATGAGG
CAGATTTGGTGCTGGCAAAAGAGACAAATATGAAATGTCTTCAAATTATAATTGCTTTTTATAAAGTGAGACTAACTTGG
CATTCTTGTCCAGAAAACAAAGCC

Alignment

ORF - retro_pvam_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 96. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQKAGK
          QN.KS..VE.AEPEEFVVE.VLD..V.NGKVEYFLKW.GFTDADNTWE.EENLD.PEL.EAFLNSQKAGK
Retrocopy QNRKSRRVETAEPEEFVVEEVLDQSVLNGKVEYFLKWTGFTDADNTWELEENLDNPELSEAFLNSQKAGK

Parental  EKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAK
          EKDGTKR..LS..ESDDSKSKKKRDAAD.PRGFARGLDPE..IGATD..GELMFL.KWKD.DEADLVLAK
Retrocopy EKDGTKRETLSGNESDDSKSKKKRDAAD*PRGFARGLDPE*VIGATDNNGELMFLIKWKDYDEADLVLAK

Parental  EANMKCPQIVIAFYEERLTWHSCPEDEA
          E.NMKC.QI.IAFY..RLTWHSCPE..A
Retrocopy ETNMKCLQIIIAFYKVRLTWHSCPENKA

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_294 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 11 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Pan troglodytes	ENSPTRG00000019003	10 retrocopies	retro_ptro_17, retro_ptro_1706, retro_ptro_1875, retro_ptro_2289, retro_ptro_2475, retro_ptro_395, retro_ptro_537, retro_ptro_630, retro_ptro_729, retro_ptro_780,
Pteropus vampyrus	ENSPVAG00000006297	2 retrocopies	retro_pvam_294 , retro_pvam_786,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,