RetrogeneDB ID: retro_pvam_414

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3002:231779..232647(+)
• Located in intron of: ENSPVAG00000006516

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSPVAG00000004645
• Aliases: None
• Description: tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766]

Sequence

>retro_pvam_414
ATGCGTGAGTGCAACTCCATCCACGTTGGCCAGGCTGCTGTTCAGATCAGCTATGCCTGCTGGGAGCTCTACTGCCTAGA
ATACAGCATCCAGCCTGATGGCCAGATGCCAAGTGACAAGACCGTTGGGAGCAGTGAGATGACTTCAACACCTTCTTCAG
TGAGACAGGTGCTGGCAAGCATGTGCCTAGGACAGTGTTCATAGACCTGGAACCCATGGTCATTAACGAAGTTCGCACTG
GCACCTACCACCAGCTCTTCCACCCCGAGCAGCTCATCACAGGCAAGGAAGACGTTGCCAGTAACTATGCTCGCGGCCAT
TATGCCTTTGCAAGGAGATCTTTGACCTTGTCTTATATCAAATTTAGAAGCTGGCTAACCAGTGCATAGGTCTTCAGGGC
TTCTTGGTTTTCCATAGCTTTGGTGGGGGAACTGGTTCCGGATTCACCTCCCTACTGATGGAATGTCTCTTTGTTGATTA
TGGCAAGAAGTCTAAGCTGGAGTTCTCCATTTACCCAGTCTCCCAGGATTCCAAAACTGTAGTTGAGCCCTACAACTCCG
TCCTCACTGCTCACATTACCCTGGAGCACTCTGATTGTGCTATCATGGTTGACAATGAAGCTATCTATAACATCTGTTAT
AGAAATCTTGATATTGAACTTCCAACTTATACTAACCTGAATAGATTGATAGGTCAAATTATATCCTCCATCACTGCTTC
CCTGACATTTGATGAAGCCCTGAATGTTTATCTGACACAATTCCCGACCAACCTAGTACCCTATTTCTGCATCCACTTCC
CTCTGGCCACTTATGCCCCTGTCATCTTTGATGAGAAAGCCTACCATGAACAGCTTGCTGTAGCAGAT

Alignment

ORF - retro_pvam_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.16 %
• Parental protein coverage: 64.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGD-DSFNTFFSETGAGKHVPRAVFVD
          MREC.SIHVGQA.VQI..ACWELYCLE..IQPDGQMPSDKT.G....D.FNTFFSETGAGKHVPR.VF.D
Retrocopy MRECNSIHVGQAAVQISYACWELYCLEYSIQPDGQMPSDKTVGSSE<DDFNTFFSETGAGKHVPRTVFID

Parental  LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIG-KEIIDLVLDRIRKLADQCTGLQGFLVF
          LEP.VI.EVRTGTY.QLFHPEQLITGKED.A.NYARGHY....KEI.DLVL..I.KLA.QC.GLQGFLVF
Retrocopy LEPMVINEVRTGTYHQLFHPEQLITGKEDVASNYARGHYAFA<KEIFDLVLYQI*KLANQCIGLQGFLVF

Parental  HSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEA
          HSFGGGTGSGFTSLLME.L.VDYGKKSKLEFSIYP..Q.S..VVEPYNS.LT.H.TLEHSDCA.MVDNEA
Retrocopy HSFGGGTGSGFTSLLMECLFVDYGKKSKLEFSIYPVSQDSKTVVEPYNSVLTAHITLEHSDCAIMVDNEA

Parental  IYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISA
          IY.IC.RNLDIE.PTYTNLNRLIGQI.SSITASL.FD.ALNV.LT.F.TNLVPY..IHFPLATYAPVI..
Retrocopy IYNICYRNLDIELPTYTNLNRLIGQIISSITASLTFDEALNVYLTQFPTNLVPYFCIHFPLATYAPVIFD

Parental  EKAYHEQLSVAE
          EKAYHEQL.VA.
Retrocopy EKAYHEQLAVAD

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_414 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
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,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,