RetrogeneDB ID: retro_tbel_4649

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_96309:3492..4207(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC8
• Ensembl ID: ENSTBEG00000012040
• Aliases: None
• Description: exosome component 8 [Source:HGNC Symbol;Acc:17035]

Sequence

>retro_tbel_4649
TTCAAAACTGTAGAAGCTGGGAAGTATTAAAGATTTCCAAAGAACTGCTGTCCTGATGGAAGAGACCTTGGTGAATTCGG
AAGCACAATTGTCACTGTAGGTTCAATTAGTACGGCAGCTGGCTCTGCTTTAACGAAGTTGGGAAACACTGCAGTAGTAT
GTGGGGTTAAAGTGGGATTTGTGGCACCACCAACAGACACTGCAATGAATGATACATTGTTCCTTTGGTGGCTCCACCTC
CCCTGTGTTCATCAAGATTTCAGCCTGGACCTCCCGGAGAAGAGGCCAAGTCGCCAGCCAGCTCATCGCAGGCGTCATTG
AAAATTCACAGGTAGTTCCAAAGGAGGACTCATGCATTTCTCCAGGAAGGCTTGCCTGGGTACTCTCCTCTGATCTCATT
TGCCTCAGCTGTGATGGCAACCTTCTGGATGCTGGCACATTTGCTGTGGTACGGGCTTTGGAAAATGTACAGTGGCTTGA
AATTATTGTACATAAAAGAACTGCATTCATAGAAGTGAATTTAAAGAACGGTTATCAGAACATTAGAGCTCATCCGGTTG
CAACGTCCTTCGCTGTGTTTGATGACACTTTACTAGTAGATGACCCTGCTGGAGAGGAGGAGCACATGGCAAAGAGGATC
CCAACTGTAGTCATGGATGAGGAGGGCAAGTGCTGTTGTCTTCACAAACCAGGGGGAGGCGGGCTGGCTGGAGCT

Alignment

ORF - retro_tbel_4649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.85 %
• Parental protein coverage: 87.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPTDTP
          FKTVE...Y.R.....NC.PDGR.LGEF..T.V..GSISTA.GSAL.KLGNT.V.CGVK..F.APPTDT.
Retrocopy FKTVEAGKY*R--FPKNCCPDGRDLGEFGSTIVTVGSISTAAGSALTKLGNTAVVCGVKVGFVAPPTDTA

Parental  -NKGYIVPNVDLPPLCSSRFRSGPPGEEA-QVASQFIADVIENSQIIQKEDLCISPGKLAWVLYCDLICL
          .N..YIVP.V..PPLCSSRF..GPPGEEA.QVASQ.IA.VIENSQ...KED.CISPG.LAWVL..DLICL
Retrocopy <NE*YIVPLVAPPPLCSSRFQPGPPGEEA<QVASQLIAGVIENSQVVPKEDSCISPGRLAWVLSSDLICL

Parental  DYDGNILDARTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTG
          ..DGN.LDA.TFA...AL.NVQ..E......TA..EVNL.K..Y.NIR.HPVATSFAVFDDTLL..DP.G
Retrocopy SCDGNLLDAGTFAVVRALENVQWLEIIVHKRTAFIEVNL-KNGYQNIRAHPVATSFAVFDDTLLVDDPAG

Parental  EEEHLATGTLTVVMDEEGKLCCLHKPGGSGLTGA
          EEEH.A....TVVMDEEGK.CCLHKPGG.GL.GA
Retrocopy EEEHMAKRIPTVVMDEEGKCCCLHKPGGGGLAGA

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_4649 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4649 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009005	2 retrocopies	retro_chof_2014, retro_chof_664,
Dasypus novemcinctus	ENSDNOG00000019133	1 retrocopy	retro_dnov_1273,
Homo sapiens	ENSG00000120699	1 retrocopy	retro_hsap_3585,
Gorilla gorilla	ENSGGOG00000011902	1 retrocopy	retro_ggor_2418,
Nomascus leucogenys	ENSNLEG00000001745	1 retrocopy	retro_nleu_1684,
Otolemur garnettii	ENSOGAG00000002745	2 retrocopies	retro_ogar_1154, retro_ogar_423,
Pongo abelii	ENSPPYG00000005287	1 retrocopy	retro_pabe_2071,
Pan troglodytes	ENSPTRG00000005790	1 retrocopy	retro_ptro_2429,
Pteropus vampyrus	ENSPVAG00000014610	1 retrocopy	retro_pvam_275,
Tupaia belangeri	ENSTBEG00000012040	9 retrocopies	retro_tbel_1492, retro_tbel_1680, retro_tbel_2932, retro_tbel_349, retro_tbel_3712, retro_tbel_4030, retro_tbel_419, retro_tbel_4649 , retro_tbel_527,