RetrogeneDB ID: retro_pvam_972

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_20003:9959..10733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CORO1B
• Ensembl ID: ENSPVAG00000008571
• Aliases: None
• Description: coronin, actin binding protein, 1B [Source:HGNC Symbol;Acc:2253]

Sequence

>retro_pvam_972
TTCCGAAAAGTGGTTTGGCATAGCAAATTCCGGCATGTGTTCGGGCAGCCAGTCAAAAATGATCAGTGTTTTGAGGCGAT
TCGAGTGTCCTGTGTCACCTGGGACAGCATTTTCTGCGCAGTCAAACCCAAGTTCCTGGCAGTGATTGTGGTGGCCAGCG
GTGCAGGCGCCTTCTTGGTGCTGCCTCTAAACAAGACGGGCCACATTGATAAGACCTACTCAACAGTGTGTGGACACATG
AAACCCGTCCTGGACATCGACTGGTGTCCTCACAACAACGAAGTCATTGCCAGCGTCTCGGAGGACTGCACAGTCGCGAT
ATGGCAGATCCCAGAGAATGGGTTGACCTCCCTGCTGACAGAACCGGTGGTGGTGCTGGAGGGGCTCACCAAGCGAGTGG
ACATCGTTATCTGGCACCCTACTGCCTGCAACCTGCTGCTTATTAGCGCAGGCTGCTATAATGCGGTGCTCACCTGGAAC
GTGAGCTAGGCGGAGGAGCTGTACCGCCTGAACAGCCTGTACCCCAACCTCATCTACAATGTCAGCTGGAACCGCAATGG
CAGCCTCTTCTGCTCCACATGCAAGGACAAGGGTGTGTGCATCACTGACCTCTTCCAGGGAATCCTGGAGACCCAGAGGG
AAAAGGCTCACGAGGGGTCCCAGCCCATGCGGGCCGTCTTTCTGGCGGATGGGAAGGCGTTCATCACAGGCTTCAGCTGC
ATGAGCGAGCAGAAGCTGGTGCTCTGAGACACAGAAAACCTCGAGAAACCGATG

Alignment

ORF - retro_pvam_972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.29 %
• Parental protein coverage: 52.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FRKVVRQSKFRHVFGQPVKNDQCYEDIRVSRVTWDSTFCAVNPKFLAVIVEASGGGAFLVLPLNKTGRID
          FRKVV..SKFRHVFGQPVKNDQC.E.IRVS.VTWDS.FCAV.PKFLAVIV.ASG.GAFLVLPLNKTG.ID
Retrocopy FRKVVWHSKFRHVFGQPVKNDQCFEAIRVSCVTWDSIFCAVKPKFLAVIVVASGAGAFLVLPLNKTGHID

Parental  KAYPTVCGHTGPVLDIDWCPHNDEVIASGSEDCTVMVWQIPENGLASPLTEPVVVLEGHTKRVGIVTWHP
          K.Y.TVCGH..PVLDIDWCPHN.EVIAS.SEDCTV..WQIPENGL.S.LTEPVVVLEG.TKRV.IV.WHP
Retrocopy KTYSTVCGHMKPVLDIDWCPHNNEVIASVSEDCTVAIWQIPENGLTSLLTEPVVVLEGLTKRVDIVIWHP

Parental  TARNVLL-SAGCDNVVLIWNVGTAEELYRLDSLHPDLIYNVSWNRNGSLFCSACKDKSVRIIDPRRGILV
          TA.N.LL.SAGC.N.VL.WNV..AEELYRL.SL.P.LIYNVSWNRNGSLFCS.CKDK.V.I.D...GIL.
Retrocopy TACNLLLISAGCYNAVLTWNVS*AEELYRLNSLYPNLIYNVSWNRNGSLFCSTCKDKGVCITDLFQGILE

Parental  SEREKAHEGARPMRAIFLADGKVFTTGFSRMSERQLALWDPENLEEPM
          ..REKAHEG..PMRA.FLADGK.F.TGFS.MSE..L.L.D.ENLE.PM
Retrocopy TQREKAHEGSQPMRAVFLADGKAFITGFSCMSEQKLVL*DTENLEKPM

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_972 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000008571	1 retrocopy	retro_pvam_972 ,