RetrogeneDB ID: retro_tbel_2460

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_111171:42356..43350(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP1
• Ensembl ID: ENSTBEG00000004386
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 1 [Source:HGNC Symbol;Acc:30292]

Sequence

>retro_tbel_2460
GGTTCTGTTGTAAATAAGCTTTATGTTCACAATGATATCTTCAGATACCAAGATGAGGTTTTTGGTGGTTTTGTCACTGA
GTCTCAGGAGGAATCTGAGGAAGAAGTAGAGGAACCTGAAGAAAGACAACAGACACCCGAGGTGGTACCTGATCATTCTG
GAACTTTCTATGATCAGAGTGTCAGCAATGTCTTGGAAGAACATTTAGAGGAGACCGTTGATGAACCAGAGCCTGATCCT
GAACCCGAACCAGAGCAAGAACCTGTATCTGAAATCTAAGAGGAAAAGTCTGAGCCAGTGTTAGAAGAAACTGCCCCTGA
GGATGCTCAGAAGAGTTCTTCTCCAGCACCTACAGATATAACTCAGACAGTACAGGAAGACTTGAGGACATTTTCTTGGG
CATCTGTAACCAGTAATAACCTTTCACCCAGTGGAGCTATTCCAGTTACTGGGATACCACCTCATGTTGTTAAAGTACCA
GCTTCACAGCCCCGTCTAGAATCAAAGCCTGAATCTCAGATCCACCACAGAGGCCTCAGAGGGATCAAAGAGTGTGGGGA
CAATGAATAAATATTCCTCCACAGAAGGGACCCAGACCAATCCGTGAGACTGGCGAGCAAGGTGATGTTGAACCCCGAAG
GATTGTGACACACTCTGATAGTCACCAACTCTTCATTGGCAACCTGCCTCATGAGGTGGACAAGTCAGAGCTTAAGATTT
CTTTCAAAATTATGGGAATGTGGTGGAGCTGCTCATTAACAGTGGTGGGAAATTATCCAATTTTGGATTTGTTGTATGTG
ATGATTCTGAGCCCATTCAGAGGATCCTTAGCAATAGGCCCATCATGTTCAGAAGTGAGGTCCACCTGAATGTCAAAGAG
AAGAAGACTTGAGCTGCCAGGGGAGGGGACCGTTGAGATAACCGCCTGCGGGGACCTGGAGACCCTCGAGATGGGCTGGG
TGGTGGAATGAGAAGTCCTCCCTGTGAAGGCATG

Alignment

ORF - retro_tbel_2460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 95.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSVANKFYVHNDIFRYQDEVFGGFVTEPQEESEEEVEEPEERQQTPEVVPDDSGTFYDQSVSNDLEEHLE
          GSV.NK.YVHNDIFRYQDEVFGGFVTE.QEESEEEVEEPEERQQTPEVVPD.SGTFYDQSVSN.LEEHLE
Retrocopy GSVVNKLYVHNDIFRYQDEVFGGFVTESQEESEEEVEEPEERQQTPEVVPDHSGTFYDQSVSNVLEEHLE

Parental  EPVAEPEPDPEPEPEQEPVSEIQEEKSEPVLEETAPEDTQKSSSPAPTDIAQTVQXXXXTFSWASVTSKN
          E.V..................I.EEKSEPVLEETAPED.QKSSSPAPTDI.QTVQ....TFSWASVTS.N
Retrocopy ETVDXXXXXXXXXXXXXXXXXI*EEKSEPVLEETAPEDAQKSSSPAPTDITQTVQEDLRTFSWASVTSNN

Parental  LPPSGAVPVTGIPPHVVKVPASQPRPESKPESQI-PPQRPQRDQRVREQRINIPPQRGPRPIRETGEQGD
          L.PSGA.PVTGIPPHVVKVPASQPR.ESKPESQI.PPQRPQRDQRV..Q.INIPPQ.GPRPIRETGEQGD
Retrocopy LSPSGAIPVTGIPPHVVKVPASQPRLESKPESQI<PPQRPQRDQRVWGQ*INIPPQKGPRPIRETGEQGD

Parental  VEPRRIVRHPDSHQLFIGNLPHEVDKSELK-DFFQNYGNVVELRINSGGKLPNFGFVVFDDSEPVQKVLS
          VEPRRIV.H.DSHQLFIGNLPHEVDKSELK.DFFQNYGNVVEL.INSGGKL.NFGFVV.DDSEP.Q..LS
Retrocopy VEPRRIVTHSDSHQLFIGNLPHEVDKSELK<DFFQNYGNVVELLINSGGKLSNFGFVVCDDSEPIQRILS

Parental  NRPIMFRGEVRLNVEEKKTRAAREGDRRDNRLRGPGGPRGGLGGGMRGPPRGGM
          NRPIMFR.EV.LNV.EKKT.AAR.GDR.DNRLRGPG.PR.GLGGGMR.PP..GM
Retrocopy NRPIMFRSEVHLNVKEKKT*AARGGDR*DNRLRGPGDPRDGLGGGMRSPPCEGM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2460 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2460 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 7 parental genes, and 21 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,
Echinops telfairi	ENSETEG00000017447	1 retrocopy	retro_etel_1488,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,
Tupaia belangeri	ENSTBEG00000004386	12 retrocopies	retro_tbel_2177, retro_tbel_2295, retro_tbel_2296, retro_tbel_2327, retro_tbel_2352, retro_tbel_2460 , retro_tbel_2461, retro_tbel_3889, retro_tbel_3928, retro_tbel_4180, retro_tbel_4190, retro_tbel_4246,
Tursiops truncatus	ENSTTRG00000009072	1 retrocopy	retro_ttru_70,