RetrogeneDB ID: retro_tbel_943

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3377:167855..168200(+)
• Located in intron of: ENSTBEG00000016394

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSTBEG00000017031
• Aliases: None
• Description: general transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:HGNC Symbol;Acc:20872]

Sequence

>retro_tbel_943
ATGGCAGCTGGGGAGAAGTGGATGTGGAAGAACAATGATGAGGAGGAGCACGTGGTTCTGGTCGTTTTCAGAAATTATTG
ATTCAGACTTTCTCTCAAAATGTGAAAATAAATGCAAGATTTTGGGAATTGACACTGAGAGGCCAATTTTGCAAGTGGAC
AACTATGTTTTTCTGGAGAATACGAAGATACTCTTGGGATCTGTGTTATATTTGAAGAAAATGTTGAACATGTGGATGCA
GAAGGCAATAACAAAACAGTGTTAAAATCTGAATGCCTCACAATGAAGAAGCTCAGAATGACAAGAACTCTTCTTACAGA
AAAGGAGGAAGGAGAAGAAAACATA

Alignment

ORF - retro_tbel_943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 55.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAGEKRIWEDDDEEEEEEQLVLV-EFSGIIDSDFLSKCENKCKILGIDTERPILQVDNYVF-AGEYEDT
          MAAGEK..W........EE..V....FS.IIDSDFLSKCENKCKILGIDTERPILQVDNYVF..GEYEDT
Retrocopy MAAGEKWMWKNN----DEEEHVVL>SFSEIIDSDFLSKCENKCKILGIDTERPILQVDNYVF<SGEYEDT

Parental  LGTCVIFEENVEHVDAEGNNKTVLKYKCHTMKKLSMTRTLLSEKKEGEENI
          LG.CVIFEENVEHVDAEGNNKTVLK..C.TMKKL.MTRTLL.EK.EGEENI
Retrocopy LGICVIFEENVEHVDAEGNNKTVLKSECLTMKKLRMTRTLLTEKEEGEENI

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_943 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_943 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001496	1 retrocopy	retro_chof_1436,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Tupaia belangeri	ENSTBEG00000017031	4 retrocopies	retro_tbel_2653, retro_tbel_3585, retro_tbel_631, retro_tbel_943 ,