RetrogeneDB ID: retro_tbel_1546

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5044:495779..496019(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIN1
• Ensembl ID: ENSTBEG00000003793
• Aliases: None
• Description: peptidylprolyl cis/trans isomerase, NIMA-interacting 1 [Source:HGNC Symbol;Acc:8988]

Sequence

>retro_tbel_1546
CGGCGGCAGATCACCTGGATGGAGAAGGAAGCTTGGGAATCCAAGGGCTACATCCAGATCAGGTCAGGAGAGGACTTGCA
GACTCTGGCCTCACAGTTCAGTAACTGCAGCTCCGCCAAGGCCAGGGAGCCCTGAGTGCCCTCACCAGCTGTCAGCTATA
AAAGTCCTTTGGAGACGCCTCATTTGCGTTGCACCAGGGGAGAGGAGCACCAGCCTCACTTCACTATTCTCAGCATCCAC

Alignment

ORF - retro_tbel_1546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.12 %
• Parental protein coverage: 50.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKAR-GDLGAFSRGQMQKPFEDASFALR-
          ...IT....EA.E...GYIQ.I.SGE.D...LASQFS.CSSAKAR.G.L.A....Q..K.F.DASFAL..
Retrocopy RRQITWMEKEAWES-KGYIQ-IRSGE-DLQTLASQFSNCSSAKAR<GALSALTSCQL*KSFGDASFALH>

Parental  TGEMSGPVFTDSGIH
          .GE...P.FT...IH
Retrocopy RGEEHQPHFTILSIH

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_1546 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1546 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006079	1 retrocopy	retro_cjac_2925,
Homo sapiens	ENSG00000127445	1 retrocopy	retro_hsap_168,
Gorilla gorilla	ENSGGOG00000006008	1 retrocopy	retro_ggor_252,
Microcebus murinus	ENSMICG00000001996	1 retrocopy	retro_mmur_1157,
Mus musculus	ENSMUSG00000032171	1 retrocopy	retro_mmus_2072,
Nomascus leucogenys	ENSNLEG00000011999	1 retrocopy	retro_nleu_980,
Pongo abelii	ENSPPYG00000009537	1 retrocopy	retro_pabe_462,
Pan troglodytes	ENSPTRG00000010452	1 retrocopy	retro_ptro_159,
Rattus norvegicus	ENSRNOG00000020474	1 retrocopy	retro_rnor_1220,
Tupaia belangeri	ENSTBEG00000003793	1 retrocopy	retro_tbel_1546 ,