RetrogeneDB ID: retro_tbel_3224

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_134336:106034..106500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE2
• Ensembl ID: ENSTBEG00000005371
• Aliases: None
• Description: non-SMC element 2, MMS21 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26513]

Sequence

>retro_tbel_3224
GGTTTCATATCCTTCATTGGTGTAGTTTATCCTCTTTTCCTTAAAAATTTCCAGACATGAATCAGCTCTGGAATGGACAG
AGCTTCTAGTTTTGCTTTGGATCTTGTGGAAATCCAGACTGAAGTGAGCAGTGAACATAGTATGGACAAAGCAATGGTTG
AATTTTCTATAATGAATCAGAAACAAACCATTATTTAAAGACTGCTCAATCTACAATAAATCATATCAAAGAAGAACATC
GAGAAAAAATACTAGACTTTAAATTACTAGTAGAGAAGAAAATTTTGGCTTTACAAAATAAGAATTCTGACACAGACTTT
CAAAATAATGAAAAATTTGTACAATTTAAACAATAGCTGAAAGACCTAAAGAAGCAATATGGTCTTCAAGCAGACAGGGA
GTCTGATGGACCTGAAGGCATTGACAAAGAAATGATTATGACCAGAGTCAGACCAAATTCATCTGT

Alignment

ORF - retro_tbel_3224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.73 %
• Parental protein coverage: 79.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFISFSGVESALSSLKNFQACISSGMDTASSVALDLVETQTEVSSEYSMDKAMVEFAIMDR-ELNHYVKA
          GFISF.GV...L..LKNFQ..ISSGMD.ASS.ALDLVE.QTEVSSE.SMDKAMVEF.IM...E.NHY.K.
Retrocopy GFISFIGVVYPLF-LKNFQT*ISSGMDRASSFALDLVEIQTEVSSEHSMDKAMVEFSIMNQ<ETNHYLKT

Parental  VQSTINHVKEERPEKIPDLKLLVEKKFMALQNKNSDADFQNNEKFVQFKQQLKDLKKQYGLQADKEADGT
          .QSTINH.KEE..EKI.D.KLLVEKK..ALQNKNSD.DFQNNEKFVQFKQ.LKDLKKQYGLQAD.E.DG.
Retrocopy AQSTINHIKEEHREKILDFKLLVEKKILALQNKNSDTDFQNNEKFVQFKQ*LKDLKKQYGLQADRESDGP

Parental  EGIDEDMIVT-QSQTNFIC
          EGID..MI.T.QSQT.FIC
Retrocopy EGIDKEMIMT<QSQTKFIC

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_3224 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3224 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009394	1 retrocopy	retro_btau_669,
Echinops telfairi	ENSETEG00000019897	1 retrocopy	retro_etel_1348,
Macaca mulatta	ENSMMUG00000003542	1 retrocopy	retro_mmul_1641,
Mus musculus	ENSMUSG00000059586	3 retrocopies	retro_mmus_1189, retro_mmus_1190, retro_mmus_3227,
Otolemur garnettii	ENSOGAG00000015798	1 retrocopy	retro_ogar_3039,
Rattus norvegicus	ENSRNOG00000003964	2 retrocopies	retro_rnor_2118, retro_rnor_701,
Tupaia belangeri	ENSTBEG00000005371	1 retrocopy	retro_tbel_3224 ,