RetrogeneDB ID: retro_tsyr_1919

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_66790:661..1004(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSTSYG00000006715
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_tsyr_1919
CTTCAGCAGAAACAAATGGTCATTGATGTCTTCACCCCAGGAAGGCAACAGTACGTAAGACAGAAATCAGGAAAAACTAG
TCAAAATGTACAAGACTACACCGGATGTCATCTTTGTATTTGAATTCAAAACTCATTTTGGCGGTGGCAAGACTACTGGC
TTTGATATGATTTATAATCTCTTGGATTATGTAAAGAAAAATGAACCCAAACATGGACTTGCAAGACATGGCCGGTATGA
GAAGAAAAAGATCTCAAGGAAGCAGTGAAAGGAACACAAGAGCAGAATGAAGAAAGTCAGGTGGACTGTAAAGGCCAATG
TTAATGCTGGCAAAAAGGCAAAG

Alignment

ORF - retro_tsyr_1919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.39 %
• Parental protein coverage: 90.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQQKQMGIDV-LHPGKATVPKAEIR-DKLSK-YKTTPDLIFEFGFRTHSGGGKTTCVDXXXXXXXXXXXX
          LQQKQM.IDV.LHP.KATV.K.EIR..KL.K.YKTTPD.IF.F.F.TH.GGGKTT..D............
Retrocopy LQQKQMVIDV<LHPRKATVRKTEIR<EKLVKMYKTTPDVIFVFEFKTHFGGGKTTGFDMIYNLLDYVKKN

Parental  XXXXXXXXHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKKAK
          ........HG.YEKKK.SRKQ.KE.K.RMKKVR.T.KANV.AGKKAK
Retrocopy EPKHGLARHGRYEKKKISRKQ*KEHKSRMKKVRWTVKANVNAGKKAK

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_1919 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 14 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017818	17 retrocopies	retro_amel_1043, retro_amel_1258, retro_amel_1303, retro_amel_1397, retro_amel_145, retro_amel_1814, retro_amel_1832, retro_amel_225, retro_amel_24, retro_amel_251, retro_amel_328, retro_amel_331, retro_amel_515, retro_amel_718, retro_amel_768, retro_amel_81, retro_amel_886,
Cavia porcellus	ENSCPOG00000020096	3 retrocopies	retro_cpor_1333, retro_cpor_14, retro_cpor_923,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pongo abelii	ENSPPYG00000002304	1 retrocopy	retro_pabe_184,
Rattus norvegicus	ENSRNOG00000010189	1 retrocopy	retro_rnor_206,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919 ,