RetrogeneDB ID: retro_tbel_3250

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_134894:48492..48936(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC1
• Ensembl ID: ENSTBEG00000004641
• Aliases: None
• Description: tetratricopeptide repeat domain 1 [Source:HGNC Symbol;Acc:12391]

Sequence

>retro_tbel_3250
GTTCCTGATCCCAAAGGCCAGCATTCTCAGAGCAAGCCACTCAAGGAGGATGAGGCTCAAACCCAGAAGGACCAGGGAGA
GGAGGAGGAGTGTTTTCATGACTGCGTGCCTCCTTTGAGGAGTCAGGAATGGATAAACTTCCAAACAGACCTGATGATGA
TGTGAATTCCTCTGAACTGGATGAAGAATGTCTGCTAGAACTGGGAAAAAAACATGCCAGATGAAGAGAAACAGAAAAGA
AGAGAAGAAAGTGCTAGGCTAAAGGAGGAGGGAAATGAGCAGTTTAAGAAAGGAGAGTATATAGAGGCTGAAAGTTCTTA
TAGTCAAGCTCTTCAGATGTGCCCATCTTACTTCCAGAAAGATAGATCCATTCTTTTTTCCAATAGAGCTGCTGCAAGGA
TGAAACAGGACAAGAAAGAGACTGCCATCAGTGACTGCAGCAAA

Alignment

ORF - retro_tbel_3250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 56.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPGPNDQHSQNKLLQDEETQWE-DQGEEE-CLLDC-SALFEEQAGVNAESKPDDAVNSSELDEEELLEL-
          VP.P..QHSQ.K.L...E.Q...DQGEEE.C..DC..A.FEE.........PDD.VNSSELDEE.LLEL.
Retrocopy VPDPKGQHSQSKPLKEDEAQTQKDQGEEEECFHDC<RASFEESGMDKLPNRPDDDVNSSELDEECLLEL>

Parental  EKHMPDEEKQKRREESARLKEEGNEQFKKGEYVEAESSYSQALQMCPSCFQKDRSILFSNRAAARMKQD-
          EK.MPDEEKQKRREESARLKEEGNEQFKKGEY.EAESSYSQALQMCPS.FQKDRSILFSNRAAARMKQD.
Retrocopy EKNMPDEEKQKRREESARLKEEGNEQFKKGEYIEAESSYSQALQMCPSYFQKDRSILFSNRAAARMKQDK

Parental  KETDISDCSK
          KET.ISDCSK
Retrocopy KETAISDCSK

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_3250 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3250 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019397	1 retrocopy	retro_etel_1659,
Myotis lucifugus	ENSMLUG00000003057	2 retrocopies	retro_mluc_1351, retro_mluc_2408,
Otolemur garnettii	ENSOGAG00000016342	1 retrocopy	retro_ogar_1052,
Tupaia belangeri	ENSTBEG00000004641	1 retrocopy	retro_tbel_3250 ,
Vicugna pacos	ENSVPAG00000012031	1 retrocopy	retro_vpac_498,