RetrogeneDB ID: retro_tsyr_245

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_6149:56918..57202(+)
• Located in intron of: ENSTSYG00000011497

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14C
• Ensembl ID: ENSTSYG00000002873
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14C [Source:HGNC Symbol;Acc:14952]

Sequence

>retro_tsyr_245
CAAGGGAAGGTCACTGTCAAGTACGATCATGAGGAGCCACGGAAGTGCCTCAACCTGGAGGAGAGGATCCTGGAGCAGCT
CACGCGCCTCTACCACTGCTAGGAAGCAAGATCCCAGAGCTGGAGATTGATGTGGATGAGCTCTTGGACATGGAAAGTGA
TGACACCCAGGCTGCCAGGGTCAAGGAACTGCTGGTTGACTGTTACAAAACCACCAAGGCCTTCATCTCTGGATTGCTGG
ACAAGATCTGAGGTATGCAGAAGCGGAGTACACCCCAAAAGAAG

Alignment

ORF - retro_tsyr_245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.29 %
• Parental protein coverage: 56.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QGKVTVKYDRKELRKRLVLEEWIVEQLSQLYGCEE-EEMPDVEIDIDDLLDADSEEERASKLQEALVDCY
          QGKVTVKYD..E.RK.L.LEE.I.EQL..LY.C.E....P..EID.D.LLD..S....A....E.LVDCY
Retrocopy QGKVTVKYDHEEPRKCLNLEERILEQLTRLYHC*E<SKIPELEIDVDELLDMESDDTQAARVKELLVDCY

Parental  KPTEEFIKELLSRIRGMRKLSPPQKK
          K.T..FI..LL..I.GM.K.S.PQKK
Retrocopy KTTKAFISGLLDKI*GMQKRSTPQKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_245 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026586	2 retrocopies	retro_btau_161, retro_btau_571,
Dasypus novemcinctus	ENSDNOG00000017261	2 retrocopies	retro_dnov_1661, retro_dnov_80,
Myotis lucifugus	ENSMLUG00000023245	2 retrocopies	retro_mluc_1095, retro_mluc_499,
Mus musculus	ENSMUSG00000040653	2 retrocopies	retro_mmus_2089, retro_mmus_3721,
Pongo abelii	ENSPPYG00000017102	4 retrocopies	retro_pabe_1880, retro_pabe_2079, retro_pabe_3001, retro_pabe_3232,
Tarsius syrichta	ENSTSYG00000002873	1 retrocopy	retro_tsyr_245 ,