RetrogeneDB ID: retro_tsyr_1714

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_55360:7328..7811(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAGR1
• Ensembl ID: ENSTSYG00000008812
• Aliases: None
• Description: PAXIP1 associated glutamate-rich protein 1 [Source:HGNC Symbol;Acc:28707]

Sequence

>retro_tsyr_1714
GAGGAGGTGGAGCTGCCCATAAATGGGCAGTCCTGGATGCTCCCGCCGTCCAAAATCCAGCAGCTTTATGAACTACTGGC
GGCCCATGGTACCCTGGAGCTTCAAGCTGAGATACTGCCGCACCAGCCTCCCATGACCGAGGGCCAGAGTGAAGAGAGAA
ATCAGATAAGGAATAGGAGGCCAAAGAAGAGGAAGAGAAAAAACTGACTACACGTGCCCATGGAATTTGACTTTGATAAT
AAGCCAGTGACACCAAAGGATGCCCTGACTGACCAGAGATGCACCCCAGGAAGCTTAGCCCGGAGCCAGAAATGGGAGGT
CCACCTGGACAAGGTCCTGTTGGATATGAAGTGACACAAGAAGCTGAAGGAGATCTTTCATACTAGGAGGGACCTCTTCA
GCCTGGACTCAAAGGACCCCAGACCCACCAGCCTCCCACTCTGGTCCTCAGGGAGCAGTCTCGTTCCCCAACAGGGGAAG
TAC

Alignment

ORF - retro_tsyr_1714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.95 %
• Parental protein coverage: 63.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEVELPADGQSWMPPPSEIQRLYELLAAHGTLELQAEILPRRPPTPEAQSEE-EKSDEEQEAKE-EEEEK
          EEVELP..GQSWM.PPS.IQ.LYELLAAHGTLELQAEILP..PP..E.QSEE.EKSD.E.EAKE.EE...
Retrocopy EEVELPINGQSWMLPPSKIQQLYELLAAHGTLELQAEILPHQPPMTEGQSEE<EKSDKE*EAKEEEEKKL

Parental  P-HMPTEFDFDDEPMTPKDALIDRRRTPGSSARSQKREARLDKVLSDMKRHKKLEEQILRTGRDLFSLDS
          ..H.P.EFDFD..P.TPKDAL.D.R.TPGS.ARSQK.E..LDKVL.DMK.HKKL.E.I..T.RDLFSLDS
Retrocopy T>HVPMEFDFDNKPVTPKDALTDQRCTPGSLARSQKWEVHLDKVLLDMK*HKKLKE-IFHTRRDLFSLDS

Parental  EDPNPTSPPLRSAGSSLFPRQRKY
          .DP.PTS.PL.S.GSSL.P.Q.KY
Retrocopy KDPRPTSLPLWSSGSSLVPQQGKY

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_1714 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007182	1 retrocopy	retro_cjac_659,
Tarsius syrichta	ENSTSYG00000008812	1 retrocopy	retro_tsyr_1714 ,