RetrogeneDB ID: retro_tbel_1233

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4214:326171..326432(+)
• Located in intron of: ENSTBEG00000010966

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R1A
• Ensembl ID: ENSTBEG00000001193
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 1A [Source:HGNC Symbol;Acc:9286]

Sequence

>retro_tbel_1233
CCTGAGGTGGACGAGACCAGATCCCTTACTCACTTCTCAAGTCCACTTTGGCTGTGTCTCCGTGACAGCGGGAGAAGTGG
GCAAGGACCACGTCCACAGTGACTTGAGTTCCAGGTGATGGTTGAACATCACTGGGGACAGCAACAGCAGGGAGAGGAGC
CTGAGGGAGCCATGAAGAGCACGGCAGGGATCTGGGAGGCCTGCCCATCTGGGATCCCGGGCACAGAAATGGAGTCAAGG
CTTGTCACCTCTGGGGCAGCC

Alignment

ORF - retro_tbel_1233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.29 %
• Parental protein coverage: 63.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PEIDE-DRIPNPLLKSTLSMSPRQRKKMTRTTPTMK-ELQMMVEHHLGQQQQ-EEPEGAAKST-GTQESC
          PE.DE.D.IP..LLKSTL..SP.QR.K..RTT.T...E.Q.MVEHH.GQQQQ.EEPEGA.KST.G..E.C
Retrocopy PEVDE<DQIPYSLLKSTLAVSP*QREKWARTTSTVT>EFQVMVEHHWGQQQQGEEPEGAMKSTAGIWEAC

Parental  PPGITDTEAESRLGTSGTA
          P.GI..TE.ESRL.TSG.A
Retrocopy PSGIPGTEMESRLVTSGAA

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_1233 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1233 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 6 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000010159	1 retrocopy	retro_fcat_1131,
Homo sapiens	ENSG00000135447	2 retrocopies	retro_hsap_1633, retro_hsap_896,
Gorilla gorilla	ENSGGOG00000008380	1 retrocopy	retro_ggor_1231,
Pongo abelii	ENSPPYG00000004608	1 retrocopy	retro_pabe_774,
Pan troglodytes	ENSPTRG00000005044	2 retrocopies	retro_ptro_1138, retro_ptro_619,
Tupaia belangeri	ENSTBEG00000001193	20 retrocopies	retro_tbel_1191, retro_tbel_1233 , retro_tbel_1251, retro_tbel_1264, retro_tbel_138, retro_tbel_1881, retro_tbel_2036, retro_tbel_2437, retro_tbel_2574, retro_tbel_2720, retro_tbel_3243, retro_tbel_3316, retro_tbel_3377, retro_tbel_3380, retro_tbel_3414, retro_tbel_3426, retro_tbel_4551, retro_tbel_537, retro_tbel_669, retro_tbel_899,