RetrogeneDB ID: retro_tbel_4230

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_7259:48640..49314(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENO3
• Ensembl ID: ENSTBEG00000002346
• Aliases: None
• Description: enolase 3 (beta, muscle) [Source:HGNC Symbol;Acc:3354]

Sequence

>retro_tbel_4230
GAAGAAGGCGGGTTTGCTCCCAATATCGAAGAGAACAAAGAAGCCTTGGAGCTGCTGAAGAATGCAGTCAGGAAGGCTGG
CTACACTGACAAGGTTGTCCTTGGCACAGACGTGGCTGCCTCTGAGTTCTTCAGGTCTAGGAAGTATGATCTGGACATTA
AGTCTCCTCATGATTTCCGCAGGTACATCACACCTGAGCAGCTGGCTGACCTGTACAAGTCCTTCATCATGGACTACCCA
GTGGTGTCTATCAAAGACCCCTTTGACCAGGATGACTGGAACACATGGCAGAAGTTCACAGCCACTGCAGGAATCCAGGT
GGTGGGAGACGATCTGACTGTGACCAACCTAAAGTGCATTGCCAAGGCCGTGGGTGAGAAGTCGTGCAACTGCCTCCTGC
TCAAAGTGAAACAGATCAGCTCTGTGACTGAGTCCCTTCAAGCGTGCAAGCTGGTGCTATCCAATGGCAGGGGTGTGAAG
GTGCCTCATTGTTCTTGGGAGACTGAAGTTACCTTCATCACTGACCTGGTGGTGGGGCTCTGCACTGGGCAGATCAAGAC
GGGTGCAACTTGCTGGTCTGAGCTCTTGCCAAGTACTACCAGCTCCTTAGAATTGAAGAGGAAGTGGGCAGCAAGACCAA
GTTTGCCAGCAGGAACTTCAGAAACCCCCTGGCC

Alignment

ORF - retro_tbel_4230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.8 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DEGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGE
          .EGGFAPNI.EN.EALELLK.A...AGY.DKVV.G.DVAASEF.R..KYDLD.KSP.D..R.IT.E.L..
Retrocopy EEGGFAPNIEENKEALELLKNAVRKAGYTDKVVLGTDVAASEFFRSRKYDLDIKSPHDFRRYITPEQLAD

Parental  LYKSFIKNYPVVSIEDPFDQDDWGTWTSFLSGVDIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIG
          LYKSFI..YPVVSI.DPFDQDDW.TW..F.....IQ.VGDDLTVTN.K.IA.AV..K.CNCLLLKV.QI.
Retrocopy LYKSFIMDYPVVSIKDPFDQDDWNTWQKFTATAGIQVVGDDLTVTNLKCIAKAVGEKSCNCLLLKVKQIS

Parental  SVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSE-RLAKYNQLMRIEEAL
          SVTES.QACKL..SNG.GV.V.H.S.ETE.TFI.DLVVGLCTGQIKTGA.C.SE..LAKY.QL.RIEE..
Retrocopy SVTESLQACKLVLSNGRGVKVPHCSWETEVTFITDLVVGLCTGQIKTGATCWSE<ALAKYYQLLRIEEEV

Parental  GDKAVFAGRKFRNPKA
          G.K..FA.R.FRNP.A
Retrocopy GSKTKFASRNFRNPLA

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_4230 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4230 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 6 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011679	2 retrocopies	retro_cjac_115, retro_cjac_177,
Dasypus novemcinctus	ENSDNOG00000011654	2 retrocopies	retro_dnov_1712, retro_dnov_75,
Macropus eugenii	ENSMEUG00000007915	25 retrocopies	retro_meug_1019, retro_meug_1341, retro_meug_1483, retro_meug_1540, retro_meug_1566, retro_meug_1605, retro_meug_170, retro_meug_1701, retro_meug_1743, retro_meug_1869, retro_meug_1905, retro_meug_1929, retro_meug_2026, retro_meug_2190, retro_meug_235, retro_meug_269, retro_meug_578, retro_meug_607, retro_meug_637, retro_meug_803, retro_meug_820, retro_meug_906, retro_meug_965, retro_meug_973, retro_meug_976,
Rattus norvegicus	ENSRNOG00000004078	1 retrocopy	retro_rnor_2228,
Tupaia belangeri	ENSTBEG00000002346	5 retrocopies	retro_tbel_1514, retro_tbel_3080, retro_tbel_3130, retro_tbel_4230 , retro_tbel_4383,
Tarsius syrichta	ENSTSYG00000007066	7 retrocopies	retro_tsyr_1019, retro_tsyr_1157, retro_tsyr_1626, retro_tsyr_1917, retro_tsyr_2043, retro_tsyr_52, retro_tsyr_534,