RetrogeneDB ID: retro_tsyr_194

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_5030:6199..6560(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSTSYG00000012508
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_tsyr_194
CTAGTGATCCCTGAGAAGTTCCCACAGATTTTACGAGTACTCAAGACCAACATCAATGGGTGGAGGATAGCCTTTGCCAT
CACTGCCATTAAGGGTTTGGGTCAAAGATATGCTCATGTGGTGTTGAGGAACGCAGACATTGACCTCATCAAGAGGGCAG
AAGAACTCACGGAGGATGAGGTGAAACGTGTGATCACCATTATGCAGAATCCACACCAGTATAAGATCCCAGACTGGTTC
TTGAACGGAAGGAAGGATGTAAAAGACAGAAAGGACAGCCAATGTTCTAGACAACAAGCTCCGTGAAGCCCTGGAGCAAC
TGAAGACGATTCGGGTCCATAGAGGGCTATGCCGCTTCTGG

Alignment

ORF - retro_tsyr_194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 98.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQ
          LVIPEKF..ILRVL.TNI.G.R.IAFAITAIKG.G.RYAHVVLR.ADIDL.KRA.ELTEDEV.RVITIMQ
Retrocopy LVIPEKFPQILRVLKTNINGWR-IAFAITAIKGLGQRYAHVVLRNADIDLIKRAEELTEDEVKRVITIMQ

Parental  NPRQYKIPDWFLNRQKDVKDGKYSQ-VLANGLDNKLREDLERLKKIRAHRGLRHFW
          NP.QYKIPDWFLN..KDVKD.K.SQ.VL.N.L....RE.LE.LK.IR.HRGL..FW
Retrocopy NPHQYKIPDWFLNGRKDVKDRKDSQ>VLDNKL----REALEQLKTIRVHRGLCRFW

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_194 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 3 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010356	1 retrocopy	retro_cjac_3061,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Tarsius syrichta	ENSTSYG00000012508	8 retrocopies	retro_tsyr_1121, retro_tsyr_1307, retro_tsyr_1627, retro_tsyr_194 , retro_tsyr_1949, retro_tsyr_2042, retro_tsyr_575, retro_tsyr_639,