RetrogeneDB ID: retro_tbel_2116

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_100874:2124..2876(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSTBEG00000013852
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, gamma isozyme [Source:HGNC Symbol;Acc:9283]

Sequence

>retro_tbel_2116
GATATTCATGGCAATACTATGACTTGCTTTGACTTTTTGAATAGGTGGTTTCTCGTCATAAAGCAACAACCTGTTCCTAG
GGGACAATGTGGCCAGGGGGGAGCAGTCATTGGAAACCATCTGCTTCTTACTGACACCCCAAATCCAATATCCCAAGAAT
TTCTTTCTTTTCGGAGGGAACCATGAAAATGTGCCTGCATCAATCGCATTTGTGGATGTTATGACGAGCGTAAAAGAAGG
CACAACATTAACGCATGGAAAACTTTCACAGCCTGTTTTAACTGTTAAAACCGATAGCAGCTATCATCGACGAGAAAATA
TTCTGCTGTCATGGAGGTTTAGCACCAGATCTTCAATCTATGGAACAGATTCAGCGAATTATGCAACCAACCAATGTGCC
AGATCAAGGTCTTCTTTGTGGTCTTTTGTGGTCTGACCCCAATAAAGATGTCTTAGGCTGGGGTGAAAATGACAGAGGAG
TGTCCTTCACATCTGGAGCAGAAGTGATTGCAAAATTTCTCCATAAGCATGATTTGGATCTGATAAGTAGAGCCCACCAG
GTGGTCGAAGATATGTATTTTTTGCCAAGAGGCAGTTAGTTACTCTGTTTTCTGCACCCAATCATTGTGGAGAATTTGAC
AATGCAGGTGCCATGATGAATGTGGACGAAACACTAATGTGTTCTCTTTCAGATTTTAAAGCCTGCAGAGAAAAAGATGC
CAAATGCCATAAGACCTGTAACACCTTCTAGG

Alignment

ORF - retro_tbel_2116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 74.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  DIHG-QYYDLLRLFE-YGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKY-PENFFLLRGNHE-CAS
          DIHG.QYYDLL.LFE..GGF...SN.LFLGD.V.RG.QSLETIC.LL...I.Y.P...F...G....CA.
Retrocopy DIHG<QYYDLL*LFE<IGGFSS*SNNLFLGDNVARGEQSLETICFLLTPQIQY>PRISFFSEGTMK>CAC

Parental  INRIYGFYDECKRRYNIKLWKT-FTDCFNCL-PIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPD
          INRI.G.YDE.KRR.NI..WKT.F...F..L.PIAAI.DEKIFCCHGGL.PDLQSMEQI.RIM.PT.VPD
Retrocopy INRICGCYDERKRRHNINAWKT<FHSLF*LLKPIAAIIDEKIFCCHGGLAPDLQSMEQIQRIMQPTNVPD

Parental  QGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLF
          QGLLC.LLWSDP.KDVLGWGENDRGVSFT.GAEV.AKFLHKHDLDLI.RAHQVVED.Y.F.........F
Retrocopy QGLLCGLLWSDPNKDVLGWGENDRGVSFTSGAEVIAKFLHKHDLDLISRAHQVVEDMY-FLPRGS*LLCF

Parental  SAP-NYCGEFDNAGAMMSVDETLMCS-FQILKPAEKKKPNATRPVTPPR
          ..P.N.CGEFDNAGAMM.VDETLMCS.FQILKPAEKK.PNA.RPVTP.R
Retrocopy LHP<NHCGEFDNAGAMMNVDETLMCS>FQILKPAEKKMPNAIRPVTPSR

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_2116 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2116 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 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Tupaia belangeri	ENSTBEG00000013852	4 retrocopies	retro_tbel_1710, retro_tbel_2116 , retro_tbel_2311, retro_tbel_4450,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,