RetrogeneDB ID: retro_tsyr_1949

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_71300:2983..3358(-)
• 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_1949
ATGTCTCTAGTGATCCTTGAGAATCTCCAGCACGTTTCACAAGTACTCAACACCAACATCAATGGGTGGCTGAAAATAGC
TTTTGCCATCACTGCCCTTAAGGGTATGGGTCGAAGATATGCTCATGTGGTGTTGAGGAAAGCAGATATTGACCTCACCA
AGAAGGCAGGAGAACTCACCAAGGATGAGGCAGAACGTGTGATCACCATTATACAGAATTCATGCCAGTGCAAGATCCCA
GACTGGTTCTTAGACAGACAGAAGGATGTAAAGGATGGGAAATACAGCCAGGTCTTGGCCAATGGTCCAGACAGCAAGCT
CCGTGAAGACCTGGAACGACTGAAGAAGATTCGGACCCATAGAGGGCTATGCCAC

Alignment

ORF - retro_tsyr_1949 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72. %
• Parental protein coverage: 98.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
          MSLVI.E..QH...VLNTNI.G..KIAFAITA.KG.GRRYAHVVLRKADID...............VITI
Retrocopy MSLVILENLQHVSQVLNTNINGWLKIAFAITALKGMGRRYAHVVLRKADIDXXXXXXXXXXXXXXXVITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRH
          .QN..Q.KIPDWFL.RQKDVKDGKYSQVLANG.D.KLREDLERLKKIR.HRGL.H
Retrocopy IQNSCQCKIPDWFLDRQKDVKDGKYSQVLANGPDSKLREDLERLKKIRTHRGLCH

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_1949 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,