RetrogeneDB ID: retro_pvam_188

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1779:210847..211633(-)
• Located in intron of: ENSPVAG00000010673

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP1
• Ensembl ID: ENSPVAG00000017250
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 1 [Source:HGNC Symbol;Acc:30292]

Sequence

>retro_pvam_188
CACACTAAGATTCACCATGTTCATGCTCATGCCACTCTGAATGACGGTGAGGTGGTCTAGGTGTTGGGTTGCTCTCTAAT
AACAACCAGGCTTTGAGGAAATTCATGCAGACATTCATACTTGCTCCTGAGGGCTCTGTTGCAAATAAGTTCTACATTCA
CAATGATATCTTCAGGTACCAAAATGAAGTCTTCGGTGGCTTTGTCACTGGCCCTCAGGAGGAATCTGAGGAAAAAGTAG
AGGAACATGAAGAAAGACAGCAGACACCTGAGATGGTACCCGATGATTATGGAATGTTCTGTAATCAGACTGTTAGCGAT
GGCTTGGAAGAATATTTAGAGGAACATGTTGTTGAACCAGAGCCTGGTTCAGAACAGAACTGGAGCAAGAACCTGTATCT
GAAATCCAAGAGGAAAAGTCTGAGTCAGCATTGGAAGAAATTGATTCTGAGGATGCTCAGAAGAGTTCTTCTCCAGCACC
TACAGGCATTGCTCAGACTGTGCAAGAAAACTTAGGACATTTTCCTGGGTGTCTGTGACCAGTAAGAACTTTCCACCCAG
GAGAGCTGTTCCAGTTACTGGGATACCACCTTATGTTAAAGTACCAGCTTCACAGCCTGAATCTCAGATTCCACCGCAGG
GGCCTCAGTGGGATCAAAGAGTACAAGAACAACAAATAAATACTCCTCCCCAGAGGGGACCTAGACCAACCAGTGAAGCT
GGTGAGAAAGGTAATGAAGAACTGGGAGACATCCTGACAATCACCAACTCATTGGCAATCTACCTC

Alignment

ORF - retro_pvam_188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.86 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HVDAHATLNDATLNDGVVVQVMG-LLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFGGFV
          H...H.....ATLNDG.VV.V.G.LLSNNNQALR.FMQTF.LAPEGSVANKFY.HNDIFRYQ.EVFGGFV
Retrocopy HTKIHHVHAHATLNDGEVV*VLG<LLSNNNQALRKFMQTFILAPEGSVANKFYIHNDIFRYQNEVFGGFV

Parental  TEPQEESEEEVEEPEERQQTPEVVPDDSGTFYDQTVSNDLEEHLEEPVAEPEPDPE-PESEQEPVSEIQE
          T.PQEESEE.VEE.EERQQTPE.VPDD.G.F..QTVS..LEE.LEE.V.EPEP..E..E.EQEPVSEIQE
Retrocopy TGPQEESEEKVEEHEERQQTPEMVPDDYGMFCNQTVSDGLEEYLEEHVVEPEPGSE<TELEQEPVSEIQE

Parental  EKSEPVLEETAPEDAQKSSSPAPTDIAQTAQED-LRTFSWASVTSKNLPPSGAVPVTGIPPHVVKVPASQ
          EKSE..LEE...EDAQKSSSPAPT.IAQT.QE..LRTFSW.SVTSKN.PP..AVPVTGIPP..VKVPASQ
Retrocopy EKSESALEEIDSEDAQKSSSPAPTGIAQTVQEN<LRTFSWVSVTSKNFPPRRAVPVTGIPPY-VKVPASQ

Parental  PRPESKPESQIPPQRPQRDQRVREQRINIPPQRGPRPIREAGEQGDVEPRRIVRHPDSHQLFI
          P.....P.....PQ..QR...V.EQ.IN.PPQRGPRP..EAGE.G..E...I.....S.....
Retrocopy PESQIPPQG---PQWDQR---VQEQQINTPPQRGPRPTSEAGEKGNEELGDILTITNSLAIYL

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_188 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Dasypus novemcinctus	ENSDNOG00000018758	3 retrocopies	retro_dnov_1492, retro_dnov_1632, retro_dnov_526,
Homo sapiens	ENSG00000145907	1 retrocopy	retro_hsap_2322,
Microcebus murinus	ENSMICG00000012235	2 retrocopies	retro_mmur_1247, retro_mmur_1469,
Mustela putorius furo	ENSMPUG00000013661	1 retrocopy	retro_mputfur_625,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Pongo abelii	ENSPPYG00000015968	1 retrocopy	retro_pabe_2104,
Pan troglodytes	ENSPTRG00000017438	1 retrocopy	retro_ptro_1696,
Pteropus vampyrus	ENSPVAG00000017250	2 retrocopies	retro_pvam_1188, retro_pvam_188 ,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,
Tarsius syrichta	ENSTSYG00000004570	1 retrocopy	retro_tsyr_1391,