RetrogeneDB ID: retro_tbel_1908

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5979:229454..229867(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000004842
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PQBP1
• Ensembl ID: ENSTBEG00000008669
• Aliases: None
• Description: polyglutamine binding protein 1 [Source:HGNC Symbol;Acc:9330]

Sequence

>retro_tbel_1908
AACTCAGAAGCTGAGGAGAAGCTGGACCGAAACCACAAGAAGCCAGACCAGGGCTATGACAAGTCGGACAGAGACCAGGA
CCATGGCTATGACAAAGTGGAAAGAGAGAGAGCAGGACAGGGAATGGGATCAGGACCGTGGGTATGACAAGGCAGACAAG
GAAGAGGGCAAAGAACGGCGCCACCCTCACCGGAAGGAGCTGGCTCCCTACCCCAAGAGCAAGAAGGCAGCAAGCCTCAA
GGACAAAGAGACCCCACGGATCCCAGCTCATACTCAGAGGCGCCCCAGGGCACATGGTCAACAGGACTCCCGAAGCAGAA
TGAGGCTAAGACAGGTGCTGACAAACAGCAGCTGGGCCCCTCTTCCAGCAGCAGCCCTACCCCTCCCCAGGGGCTGTGCT
CCGGGCCAATGCT

Alignment

ORF - retro_tbel_1908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SDRGHEKPDRSHDKSDRGHDKSDRDRDRGYDKVDRER-ERDRERDRDRGYDKADREEGK-ERRHHRREEL
          .....EK.DR.H.K.D.G.DKSDRD.D.GYDKV.RER..R.....R..G.....R...K.ERRH..R.EL
Retrocopy NSEAEEKLDRNHKKPDQGYDKSDRDQDHGYDKVERER<SRTGNGIRTVGMTRQTRKRAK<ERRHPHRKEL

Parental  APYPKSKKAASRKDEELDPMDP-SSYSDAPRGTWSTGLPKRNEAKTGAD-TTAAGPLFQQRPYPSPGAVL
          APYPKSKKAAS.KD.E..P..P.SSYS.AP.GTWSTGLPK.NEAKTGAD..TAAGPLFQQ.PYPSPGAVL
Retrocopy APYPKSKKAASLKDKE-TPRIP<SSYSEAPQGTWSTGLPKQNEAKTGAD<QTAAGPLFQQQPYPSPGAVL

Parental  RANA
          RANA
Retrocopy RANA

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_1908 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1908 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004165	2 retrocopies	retro_meug_1293, retro_meug_435,
Mus musculus	ENSMUSG00000031157	1 retrocopy	retro_mmus_891,
Rattus norvegicus	ENSRNOG00000007766	1 retrocopy	retro_rnor_2326,
Tupaia belangeri	ENSTBEG00000008669	1 retrocopy	retro_tbel_1908 ,