RetrogeneDB ID: retro_pvam_166

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1726:157731..158525(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSPVAG00000001449
• Aliases: None
• Description: replication protein A2, 32kDa [Source:HGNC Symbol;Acc:10290]

Sequence

>retro_pvam_166
GGATTTGAAAGCTATAGCAGCTCCACCTTTAGGGGAGCCAGTGGCTACACACAGTCCCCTGTGGGCTTTGGATCACCGGC
ACCTTCCCAGGCTGAAAAAAAATCATGAGCCCAAGCCCAGCACATTGTGCTCTGTACCATATCACAGCTGCTTTCTGCTA
CTCTGGTTGATGAAGTGTTCAGAATTGAGAATGTTGAGATTTCTTCACAGGTAACTATTGTGGGGATAATCAGACATGCA
GAGAGCTCTAACATTGTTTAGAAATAGACAACATGACAGCTGCACCCATGGATGTTCGCCAGTGGGTTGACACAGATGAC
ACCAGTGGTGAAAACCCGGTGGTTCCTCCAGAAACATATGTGAAAATGGCTGGCCATCTGAGCTCTTTTCAGAACAACAA
AAGCCTGATAGCCTTTAAGATCATGCCCCTGGAGGATATGAATGAGTTCACTGCACATATTCTGGAAGTAGTGAATGCAC
ACATGACACTCAGCAAAGCTAACAGCCAGCCTTCAGCAGGGAGAGCACCCATCAGCAATCCAGGAATGCGTGAAGCAGGG
AACTCTGGTAGGAATAGCTTCATGCCAGTAAATGGCCTCACTGTGGCCCAAAACCAGGTACTGAATTTGATTAAGGCTTG
CCCAAGACCTGAAGTATTGAACTTTCACGAACTCAAGAACCAGCCCCAACACATGACTGTAGTCTCAATCAAGCAAGCTG
TGGGCTTTCTAAGCAACGAGGGACACATCTATTCCACTGTGAATGATGATCATTTTAAATCCACAGACGCAGAA

Alignment

ORF - retro_pvam_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 77.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFESYGNSTFGGAGGYPRSPGGFESPSPSQAEKKSRSRAQHIVPCTISQLLSATLVDEVFRIGNVEI--Q
          GFESY..STF.GA.GY..SP.GF.SP.PSQA...S...AQHIV.CTISQLLSATLVDEVFRI.NVEI..Q
Retrocopy GFESYSSSTFRGASGYTQSPVGFGSPAPSQAXXXS*AQAQHIVLCTISQLLSATLVDEVFRIENVEISSQ

Parental  VTIVGIIRHAEKAPTNIVYK-IDDMTAAPMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRSFQNKKSLV
          VTIVGIIRHAE....NIV.K.ID.MTAAPMDVRQWVDTDDTSGEN.VVPPETYVK.AGHL.SFQN.KSL.
Retrocopy VTIVGIIRHAESS--NIV*K<IDNMTAAPMDVRQWVDTDDTSGENPVVPPETYVKMAGHLSSFQNNKSLI

Parental  AFKIMPLEDMNEFTAHILEVVNAHMTLNKANSQPSRGRASISNPGMGEAGNFGGNSFMPVNGLTVAQNQV
          AFKIMPLEDMNEFTAHILEVVNAHMTL.KANSQPS.GRA.ISNPGM.EAGN.G.NSFMPVNGLTVAQNQV
Retrocopy AFKIMPLEDMNEFTAHILEVVNAHMTLSKANSQPSAGRAPISNPGMREAGNSGRNSFMPVNGLTVAQNQV

Parental  LNLIKACPRPEGLNFHKLKNQLQHMTVVSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE
          LNLIKACPRPE.LNFH.LKNQ.QHMTVVSIKQAV.FLSNEGHIYSTV.DDHFKSTDAE
Retrocopy LNLIKACPRPEVLNFHELKNQPQHMTVVSIKQAVGFLSNEGHIYSTVNDDHFKSTDAE

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_166 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 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166 ,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tarsius syrichta	ENSTSYG00000010706	2 retrocopies	retro_tsyr_1184, retro_tsyr_1806,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,