RetrogeneDB ID: retro_tbel_4383

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_79787:1095..2398(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000004440
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_4383
ATGTCTATTCTCAAGATCCATGCCAGAGAGATCTTCGACTCTCGTGGGATCCCCACTGTTGAGGTTGATCTGGATACCTC
AAAAGGTCTCTTCAGAGCTGCTGTGCCCAGTGGTGCCTCAATTGGGATCTATGAGGCCCTGGAACTGCGGGACAATGATA
AGACTCGCTACATGGGAAAGGGTGTCTCAAAGGCTGTTGAGCACATCAATAAAACTATTGCGCCTGCCCTGGTTAGCAAG
AAACTCAACGTTGTGGAACAGGAGAAGATTGACAAACTGATGATCGAGACGGACGGAATGGAAAACAAATCTAAGTTTGG
TGTGAATGCCATCCTGAGGGTGTCCCTTGCTGTCTGCAAAGCTGGAGCTGTTGAGAAGGGGGTGCCCCTATACCGGCACA
TTGCCGACTTGGCGGGCAATTCTGAAGTCATCCTGCCAGTTCCAGCCTTCAATGTGATCAGTGGTGGCTCTCATGCTGGC
AACAAGCTGGCCATGCAGGAGTTCATGATCCTCCCCGTGGGTGCAGCCAACTTCAGGGAAGCCATACGCATTTGGAGTGG
AAGTTTACCACAACCTGAAGAAAGTCATCAAGGAAAAATATGGGAAAGATGCCACCAACGTGGGTGACGAAGGTGAGTTT
GCTCCTAATATCCTGAAGAACAAAGAAGCCCTGGAGCTGCTGAAGGATGTGATTGCAAAGGCTGGTTATTCTGACAAGGT
TGTCATTGGCATGGACGTGGCTGCCTCTGAGTTCTTCAGGTCTGGGAAGTACGATCTGGACTTTAAGTCTCCTGATGATG
CCAGCAGGTACATCACACCTGACCAGCTGGCTGACCTGTACAAGTCCTTCATCAAGGACTACCCAGTGGTGTCTATCGAA
GACCCCTTTGATCAGGATGGCTGGAATGCATGGCAGAAGTTCACAGACACTGCGGAAATCCAGGTGGTGGGGGACAATCT
CACTGTGACCAACCCAAAGCGCATTGCCAAGGCCATGGGTGAGAAGTCATGCAACTGCCTCCTGCTCAAAGTGAACCAGA
TTGGCTCCATAACCGAGTCCCTTCAGGCATGCAAGCTGGCCCAGTCCAATGGCTGGGGGCATGATGGTGTCTCATCATTC
CGGGGAGACTGAAGATACCTTCATTGCTGACCTGGTGGTGGGACTCTGCACTGGGCAGATCAAGACTGGTGCACCTTGTC
TGTCTGAGCACTTGGCCAAGTACAACCAGCTCCTCAGAATTGAAGAGGAACTGGGCAGCAAGGCAAGTTTGCCGGCAGGA
ACTTCAGAAACCCCCTGACCAAG

Alignment

ORF - retro_tbel_4383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKSRYLGKGVLKAVEHIN
          M...KI.AREI.DSRG.PTVEVDL.T.KG.FRAAVPSGAS.GIYEALELRD.DK.RY.GKGV.KAVEHIN
Retrocopy MSILKIHAREIFDSRGIPTVEVDLDTSKGLFRAAVPSGASIGIYEALELRDNDKTRYMGKGVSKAVEHIN

Parental  KTLGPALLEKKLSVVDQEKVDKFLIELYGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGN
          KT..PAL..KKL.VV.QEK.DK..IE..G.ENKSKFG.NAIL.VSLAVCKAGA.EKGVPLYRHIADLAGN
Retrocopy KTIAPALVSKKLNVVEQEKIDKLMIETDGMENKSKFGVNAILRVSLAVCKAGAVEKGVPLYRHIADLAGN

Parental  PDLVLPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFKEAMRI-GAEVYHHLKGVIKAKYGKDATNVGD
          ....LPVPAFNVI.GGSHAGNKLAMQEFMILPVGA..F.EA.RI.G.EVYH.LK.VIK.KYGKDATNVGD
Retrocopy SEVILPVPAFNVISGGSHAGNKLAMQEFMILPVGAANFREAIRI>GVEVYHNLKKVIKEKYGKDATNVGD

Parental  EGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGEL
          EG.FAPNIL.N.EALELLK..I..AGY.DKVVIGMDVAASEF.R.GKYDLDFKSPDD..R.IT...L..L
Retrocopy EGEFAPNILKNKEALELLKDVIAKAGYSDKVVIGMDVAASEFFRSGKYDLDFKSPDDASRYITPDQLADL

Parental  YKSFIKNYPVVSIEDPFDQDDWGTWTSFLSGVDIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIGS
          YKSFIK.YPVVSIEDPFDQD.W..W..F.....IQ.VGD.LTVTNPKRIA.A...K.CNCLLLKVNQIGS
Retrocopy YKSFIKDYPVVSIEDPFDQDGWNAWQKFTDTAEIQVVGDNLTVTNPKRIAKAMGEKSCNCLLLKVNQIGS

Parental  VTESIQACKLAQSNGW-GVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEALG
          .TES.QACKLAQSNGW.G.MVSH.SGETEDTFIADLVVGLCTGQIKTGAPC.SE.LAKYNQL.RIEE.LG
Retrocopy ITESLQACKLAQSNGW>GMMVSHHSGETEDTFIADLVVGLCTGQIKTGAPCLSEHLAKYNQLLRIEEELG

Parental  DKA-VFAGRKFRNPKAK
          .KA..FAGR.FRNP..K
Retrocopy SKA<KFAGRNFRNPLTK

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_4383 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4383 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,