RetrogeneDB ID: retro_pvam_1283

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_5523:93467..94812(+)
• Located in intron of: None

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_1283
ATGCGTGAGTGCATCTCCATCTAGGCTGGCCAGGCTGGTGTTCGGATTGGCAATGCCTGCTGGGAGCTTTACTGCCTAGA
ACATGGCATCCAGCCTGATGGCCAGATGCCAAGTGACGAGACCATTGGGTGAGGAAGACGACTCCTTCAACACCTTCTTC
AGTGAGACAGGCACTGGCAAGCATATGCCCAGGACAGTATTTGTAGACCTGGAATCCATGGTCATTGATGAAGTTTGCAT
TGGCACCTATCGCCAGCTCTTCCACCCCAAGCAGCTCATCACAGGCAAGGAAGATGCCACCAATAACTATGCTTGCAGGC
ACTACACCATTGGCAAGGAGATCATTGATCTTGTCTTGGACCGAATTCAGAAGCTGGCTGACCAATGCACAGGTCTTTAG
GGCTTCTTGGTTTTCCATAGCTTTGGTGGGGAAACTGGTTCTGGGTTCACATCCCTGCTGATGAAACATCTCTCTGTCGA
TTATGTCAAGAAGTCCAAGCTGGAGTACTCCATTTACCCAGGCCCCCAAGTTTCCACAGCTGTAGTTGGGCCCTACAACT
CCATCTTCACTACCCACACCACCGCAGAGCACTCTGATTGTGCCTTCATGGTTACAAGGAGGCCATCTATGACATCTGTC
ATAGAAATCTTGATATTGAGTGCTCAACCTATACTAACCTGAATAGATTGATAGGTCGAATTGTATCCTCCATCATTACT
TCCCTGAGATTTGATGGAGTCTTGAATGTTGACCTGACAGAATTCCAAACCAACCTAGTGCCCCATCCCCACATCCACTT
CTCTCTGGCCACTTATGCCCCTGTCATCTCTGCTGAGAAATCCTACTATGAACAGCTTTCTGTAGCAGAGATCACCAATG
TTGAGCTGGCCAACCAGATAGTAAAATGTGACTCTCACCATAATAAATACATGGCTTGCTGTTTATTATACTATGGGGAC
GTGGTTCCCAAAGATGTCAATGCTGCATTGCCACCATCAAGACCAAGCGTACCATCCAGTATGTGGACTGGTACCCCACT
GGCTTCAAAGTTAGCATTAATTACCAGCCTCCCTCCGTGGTACCTGGTGGAAACCTAGCCAAGTACAGCGAGCTGTGTGC
ATGCTGAGCAACACCACAGCTATTGTTGAGGCCTGGGCTTGCCCGGACCACAAGTTTGACTCGATGTATGCCAAGCGTGC
CTTTGTTCACCAGTACGTGGGTGAGGGCATGGAGGAAGGAGAGTCTTCTGAGGCCCGTGAGGACATGGCTGCCCTTGAGA
AGAATTATGAGGAGGTTGGTGTGGATTCTGTTGAAGGAGAGGGTGAGGAAGAAGGAGAAGAATAC

Alignment

ORF - retro_pvam_1283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGG-DDSFNTFFSETGAGKHVPRAVFVD
          MRECISI..GQAGV.IGNACWELYCLEHGIQPDGQMPSD.TIG.G.DDSFNTFFSETG.GKH.PR.VFVD
Retrocopy MRECISI*AGQAGVRIGNACWELYCLEHGIQPDGQMPSDETIG*G>DDSFNTFFSETGTGKHMPRTVFVD

Parental  LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFH
          LE..VIDEV..GTYRQLFHP.QLITGKEDA.NNYA..HYTIGKEIIDLVLDRI.KLADQCTGL.GFLVFH
Retrocopy LESMVIDEVCIGTYRQLFHPKQLITGKEDATNNYACRHYTIGKEIIDLVLDRIQKLADQCTGL*GFLVFH

Parental  SFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVD-NEA
          SFGG.TGSGFTSLLM..LSVDY.KKSKLE.SIYP.PQVSTAVV.PYNSI.TTHTT.EHSDCAFMV...EA
Retrocopy SFGGETGSGFTSLLMKHLSVDYVKKSKLEYSIYPGPQVSTAVVGPYNSIFTTHTTAEHSDCAFMVT<KEA

Parental  IYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISA
          IYDIC.RNLDIE..TYTNLNRLIG.IVSSI..SLRFDG.LNVDLTEFQTNLVP.P.IHF.LATYAPVISA
Retrocopy IYDICHRNLDIECSTYTNLNRLIGRIVSSIITSLRFDGVLNVDLTEFQTNLVPHPHIHFSLATYAPVISA

Parental  EKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAA-IATIKTKRTIQFVDWC
          EK.Y.EQLSVAEITN...E.ANQ.VKCD..H.KYMACCLLY.GDVVPKDVNAA.IATIKTKRTIQ.VDW.
Retrocopy EKSYYEQLSVAEITNV--ELANQIVKCDSHHNKYMACCLLYYGDVVPKDVNAA<IATIKTKRTIQYVDWY

Parental  PTGFKVGINYQPPTVVPGGDLAK-VQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEG
          PTGFKV.INYQPP.VVPGG.LAK.VQRAVCMLSNTTAI.EAWA..DHKFD.MYAKRAFVH.YVGEGMEEG
Retrocopy PTGFKVSINYQPPSVVPGGNLAK<VQRAVCMLSNTTAIVEAWACPDHKFDSMYAKRAFVHQYVGEGMEEG

Parental  EFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          E.SEAREDMAALEK.YEEVGVDSVEGEGEEEGEEY
Retrocopy ESSEAREDMAALEKNYEEVGVDSVEGEGEEEGEEY

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_1283 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 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,