RetrogeneDB ID: retro_pvam_929

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_17261:11559..12351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1C
• Ensembl ID: ENSPVAG00000004646
• Aliases: None
• Description: tubulin, alpha 1c [Source:HGNC Symbol;Acc:20768]

Sequence

>retro_pvam_929
ATGAGTCAGTGCATCGCTTCCATGTTGGCCATGGTGGTGTCCAGATCAGGAGTGCCTGCTGAGAACTATACTGCCTGGAA
CATGGTATCCAGCCTGATGGCCAGATGCCAAATGACAAGACCATTGGAGGAGGAGTTGACTCCTTCAACACTTTCTTCAG
TGGGACAGGTGCTGGCAAACACATGCCCAAGGCAGTGTTTGTAGACCTGGAACCCACAGTCATTGATGGAGTTTGCACTG
GCAACTACTGCTATGCGTGCTTCCGCCCTGAGCAGCTCCTCACAGGCAAGGAAGATGCTGCCAACAACTACTCCTTGCAG
ACACACACCATCAGCAAAGAGATCAATGGCTGTCTGGACCATTTCAGAGCTGTCAACCAGTACACAGGTCTCAGGACTCT
TAATTTTGCACAGCTTTGGTGGGGGGAACTGATTCTCAGTTCACCTCCTGCTGGTGGAACATCTCTCTGTCTATTATGGT
AAGAAGTCCAAGCTGGAGTTCTCCATTTACTCAGCCCCATAGGTTTCCGCAGCTGTAGTTGAGCCCTACAACTCCATCCT
CACCACCCACACCACTCTGGAGCACTCTGATTGTGCCCTCCTGGTTGACAACGAGGCCATCTATGACATTTGTCGTAGAA
ATCTCGACATTAAGCGCCTGACCTACACTAATCTTAACCGTGTTATTAGCTAGATAGTGTCCTCCATCACCACTTCACTC
ATATCTGATGGAGCCCTGAATGTTGATCTGACAAAATTCCAGACCAATCTGGGTCCACTTCCTTCTGGCCAC

Alignment

ORF - retro_pvam_929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 60.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRECIS-IHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVD
          M..CI...HVG..GVQI..AC.ELYCLEHGIQPDGQMP.DKTIGGG.DSFNTFFS.TGAGKH.P.AVFVD
Retrocopy MSQCIA<FHVGHGGVQIRSAC*ELYCLEHGIQPDGQMPNDKTIGGGVDSFNTFFSGTGAGKHMPKAVFVD

Parental  LEPTVIDEVRTGTY-RQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVF
          LEPTVID.V.TG.Y....F.PEQL.TGKEDAANNY.....TI.KE.I...LD..R....Q.TGL......
Retrocopy LEPTVIDGVCTGNYCYACFRPEQLLTGKEDAANNYSLQTHTISKE-INGCLDHFRAV-NQYTGLRTLNFA

Parental  HSFGG-GTGSGFTS-LLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDN
          ....G.GT.S.FTS.LL.E.LSV.YGKKSKLEFSIY.AP.VS.AVVEPYNSILTTHTTLEHSDCA..VDN
Retrocopy QLWWG<GTDSQFTS<LLVEHLSVYYGKKSKLEFSIYSAP*VSAAVVEPYNSILTTHTTLEHSDCALLVDN

Parental  EAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIH
          EAIYDICRRNLDI.R.TYTNLNR.IS.IVSSIT.SL..DGALNVDLT.FQTNL.P.P..H
Retrocopy EAIYDICRRNLDIKRLTYTNLNRVIS*IVSSITTSLISDGALNVDLTKFQTNLGPLPSGH

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_929 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Pteropus vampyrus	ENSPVAG00000004646	1 retrocopy	retro_pvam_929 ,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,