RetrogeneDB ID: retro_tbel_3429

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_140158:147851..148077(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000001443
• Aliases: None
• Description: None

Sequence

>retro_tbel_3429
TCACTGCTGCAGGTGGCTCTACTCTGTGTCATTGCCATGATGGTCCTTCACAAGGAGCACTTCAAGAACATTGGCTGGGG
AATAGCTCAGGGAATTGGTGGATTTGGAGAAGAGCCAGGAATTTAAATTTCAGCTAATGAACCTCATTTGGTCTGTAAGA
GCTATGATGAGAGTTCCATTGATAATAGTAAACTCAATTGCAGTTGTATTACTTTTATTATTTGGG

Alignment

ORF - retro_tbel_3429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 92.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLLQAALLCVNAIAVLHEERFLKNIGWATDQGIGGFGEEPGI-KSQLMNLIRSVRTVMRVPLIIVNSVAI
          SLLQ.ALLCV.A..VLH.E.F.KNIGW...QGIGGFGEEPGI.K.QLMNLI.SVR..MRVPLIIVNS.A.
Retrocopy SLLQVALLCVIAMMVLHKEHF-KNIGWGIAQGIGGFGEEPGI>KFQLMNLIWSVRAMMRVPLIIVNSIAV

Parental  VLLLLFG
          VLLLLFG
Retrocopy VLLLLFG

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_3429 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3429 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032961	1 retrocopy	retro_btau_13,
Callithrix jacchus	ENSCJAG00000004610	1 retrocopy	retro_cjac_3333,
Echinops telfairi	ENSETEG00000000303	1 retrocopy	retro_etel_1526,
Homo sapiens	ENSG00000134049	1 retrocopy	retro_hsap_1156,
Gorilla gorilla	ENSGGOG00000027939	1 retrocopy	retro_ggor_903,
Mus musculus	ENSMUSG00000090000	1 retrocopy	retro_mmus_150,
Nomascus leucogenys	ENSNLEG00000011450	1 retrocopy	retro_nleu_2504,
Otolemur garnettii	ENSOGAG00000016626	1 retrocopy	retro_ogar_2152,
Pongo abelii	ENSPPYG00000009141	3 retrocopies	retro_pabe_2850, retro_pabe_2851, retro_pabe_962,
Pan troglodytes	ENSPTRG00000010002	1 retrocopy	retro_ptro_791,
Tupaia belangeri	ENSTBEG00000001443	4 retrocopies	retro_tbel_1530, retro_tbel_2783, retro_tbel_3343, retro_tbel_3429 ,
Tursiops truncatus	ENSTTRG00000001019	1 retrocopy	retro_ttru_1930,