RetrogeneDB ID: retro_tbel_1958

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_6064:1597..2118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSTBEG00000013764
• Aliases: None
• Description: tropomyosin 3 [Source:HGNC Symbol;Acc:12012]

Sequence

>retro_tbel_1958
GCTGAGGCTCAAGTAGCCTCCTTGAACTGTGGGATCCAGCTGGTTAAGGAGGAGCTGGATCCTGCTCAGGAGCCCCTGGA
CACTGCCCTGCAAAAGCTGAAGAAGGTGGAAAAAGCTGTTGGTGAGATGAGAGTTGTATGAAGGTTATTGAAAACTGGGC
CTTAAAATACAAGGAAAAGATGGAACTCCAAGAAATCCTACTCAAAGAAGCGAAGCACATGGTAGAAGAGGCAGAGAGGC
CCTGTGAAGAGGTGGCTGTAAGCTGGCGATTATTGAAGACTTGGCGCACGCCAAGAACCAAGCTCAACTAGCAGAGTTCC
ATGGCGGGGAGATGGGTGAGCGCATCAAACGGATGGACCAGAAACCAAAGTGTCTGAGTGCCGCCGGGGGAAACACTGTC
AGAAAGAAGGCACATAGGAGGCAGAGCAGATTTTTACTGTTGAACTCAAGAAAGCAGAGACCTTGTTGAGTTCGCTGAGA
TGTTGGTAGCCAAACTGGAAAAGACAATCGACCATTTGGAA

Alignment

ORF - retro_tbel_1958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.67 %
• Parental protein coverage: 68.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADE-SERCMKVIENRALKDEEKMELQEIQLK
          AEA.VASLN..IQLV.EELD.AQE.L.TALQKL...EKA..E..E.CMKVIEN.ALK..EKMELQEI.LK
Retrocopy AEAQVASLNCGIQLVKEELDPAQEPLDTALQKLKKVEKAVGE<DESCMKVIENWALKYKEKMELQEILLK

Parental  EAKHIAEEADRKYEEVA-RKLVIIEGDLERTEERAELAESKCSELEEELKNVTNNLKSL-EAQAEKYSQK
          EAKH..EEA.R..EEVA..KL.IIE.DL......A.LAE....E..E..K......K.L.E....K..QK
Retrocopy EAKHMVEEAERPCEEVA<CKLAIIE-DLAHAKNQAQLAEFHGGEMGERIKRMDQKPKCL<ECRRGKHCQK

Parental  EDKYEEEIKILTDKLKEAET-RAEFAERSVAKLEKTIDDLE
          E...E.E..I.T..LK.AET...EFAE..VAKLEKTID.LE
Retrocopy EGT*EAE-QIFTVELKKAET<LVEFAEMLVAKLEKTIDHLE

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_1958 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1958 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 2 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000012927	7 retrocopies	retro_tbel_1435, retro_tbel_2468, retro_tbel_3663, retro_tbel_3709, retro_tbel_3872, retro_tbel_4651, retro_tbel_482,
Tupaia belangeri	ENSTBEG00000013764	1 retrocopy	retro_tbel_1958 ,