RetrogeneDB ID: retro_tsyr_1922

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_67162:1990..2324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUSC2
• Ensembl ID: ENSTSYG00000010483
• Aliases: None
• Description: tumor suppressor candidate 2 [Source:HGNC Symbol;Acc:17034]

Sequence

>retro_tsyr_1922
GGCGCCAGGAACTCCAAAGCTCGGGGCCTGTGGCCCTTTGCTTTGGCGGCAGGGGGTGGCAACTCAGCTTTGGTGCGGCT
TTTACTCAGCTTTGGTGCGGCCTCAAGGCCGAGTCGTACCCCGCTTGGTATTCACGCACCGCGGCTCCATGATCTGTGAT
GAAGATGGGGATCTGGCTCACGAGTTCTATGAGTTTTTCGTCACCAATCGTCACCAAGAACGGGCAGAAGCTGGCCAAGC
TGAGGCGTGTGCATAGGAATCTGATTCTTCAGGGCATCGTGAAGCTGGATCCCCCCGCCTCCACGTGGATTTTCCTGTGA
TCCTCTATGAGGTG

Alignment

ORF - retro_tsyr_1922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.83 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GASGSKARGLWPFASAAGGGNPEAA-GAEQALVRPRGRAVPPFVFTRRGSMFYDEDGDLAHEFYEETIVT
          GA..SKARGLWPFA.AAGGGN.....G...ALVRP.GR.VP..VFT.RGSM..DEDGDLAHEFYE...VT
Retrocopy GARNSKARGLWPFALAAGGGNSALV>GFYSALVRPQGRVVPRLVFTHRGSMICDEDGDLAHEFYE-FFVT

Parental  KNGQKRA-KLRRVHK---NLIPQGIVKLDP-PRIHVDFPVILYEV
          ...Q.RA.KL........NLI.QGIVKLDP.PR.HVDFPVILYEV
Retrocopy NRHQERA>KLAKLRRVHRNLILQGIVKLDP<PRLHVDFPVILYEV

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_1922 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590,
Felis catus	ENSFCAG00000031595	1 retrocopy	retro_fcat_1831,
Myotis lucifugus	ENSMLUG00000002499	1 retrocopy	retro_mluc_874,
Otolemur garnettii	ENSOGAG00000008080	3 retrocopies	retro_ogar_2293, retro_ogar_2714, retro_ogar_3421,
Tarsius syrichta	ENSTSYG00000010483	2 retrocopies	retro_tsyr_1922 , retro_tsyr_2132,
Vicugna pacos	ENSVPAG00000007903	1 retrocopy	retro_vpac_221,