RetrogeneDB ID: retro_tsyr_535

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_135117:813..1413(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSTSYG00000008569
• Aliases: None
• Description: ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]

Sequence

>retro_tsyr_535
GGTTATGTGGTCCAAATCAATGGTGGGAATGATAAAAAAAGTCTTCCCCATAAAGCAGGGTATCTTGGCCCATGACCGTG
CCCACTTGCTGCTGAGTAAGGGACATTACTGTTATAGACCAAGGAGAACTGGAGAAAGAAAATACAAATCTATTTGCGGT
TGCATTATGGATGCCAATCTGAGTGTTCTAAACTTGGTTATTATAAAAAAGGGAGAGAAGGATCTTCCTGGACTAATACT
ATGGTGTCTAATTGTCTGGGGCCCAAAAAAGCTAGCAGAATCTGCAAACTTTTCAATCTCTCTAGAGGAGATGATGTCCT
CTAATACGTTGCAAGAAAGCTCTTAAACAAAGAAGGTAAGAAACCTAGGACCAAAGCACCTAAGATTCAGCGTCTCGTTA
CTCCATGTGTTCTAGAACACAACCACTGGCATATTGCTCTGAAGAGACAGCATAATAAGAAAAATAAGGAAAAGGCCACA
GAATATACTGAAGTTTTGGTCAAGAGCATGAAGGAGGCCAAAGAAATACAGGAACAGATTGCCAAAAGATGCGGACAGTC
TTTGTGAGTTTCTACTTATAAGTCTAAATCTAGTCAAAAA

Alignment

ORF - retro_tsyr_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.78 %
• Parental protein coverage: 81.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GYVVRISGGNDKQG-FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVK
          GYVV.I.GGNDK...FP.KQG.L.H.R..LLLSKGH.CYRPRRTGERK.KS..GCI.DANLSVLNLVI.K
Retrocopy GYVVQINGGNDKKS>FPIKQGILAHDRAHLLLSKGHYCYRPRRTGERKYKSICGCIMDANLSVLNLVIIK

Parental  -KGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRV
          .KG.......T.T.V...LGPK.ASRI.KLFNLS..DDV..YV.RK.LNKEGKKPRTKAPKIQRLVTP.V
Retrocopy <KGREG-SSWTNTMVSNCLGPKKASRICKLFNLSRGDDVL*YVARKLLNKEGKKPRTKAPKIQRLVTPCV

Parental  LQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK
          L.H....IALK.Q..KKNKE.A.EY...L.K.MKEAKE..QEQIAKR....SL..ST.KS.SSQK
Retrocopy LEHNHWHIALKRQHNKKNKEKATEYTEVLVKSMKEAKE-IQEQIAKRCG-QSL*VSTYKSKSSQK

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_535 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 10 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Echinops telfairi	ENSETEG00000001584	18 retrocopies	retro_etel_1143, retro_etel_1281, retro_etel_1410, retro_etel_1430, retro_etel_1575, retro_etel_167, retro_etel_1822, retro_etel_188, retro_etel_1964, retro_etel_2004, retro_etel_2041, retro_etel_2194, retro_etel_263, retro_etel_337, retro_etel_378, retro_etel_541, retro_etel_809, retro_etel_825,
Ficedula albicollis	ENSFALG00000003078	1 retrocopy	retro_falb_24,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Myotis lucifugus	ENSMLUG00000007588	27 retrocopies	retro_mluc_1041, retro_mluc_1146, retro_mluc_1169, retro_mluc_1393, retro_mluc_1411, retro_mluc_1448, retro_mluc_1472, retro_mluc_1532, retro_mluc_1566, retro_mluc_1593, retro_mluc_1629, retro_mluc_1635, retro_mluc_1723, retro_mluc_1799, retro_mluc_1909, retro_mluc_1928, retro_mluc_1933, retro_mluc_2110, retro_mluc_2129, retro_mluc_490, retro_mluc_493, retro_mluc_514, retro_mluc_557, retro_mluc_652, retro_mluc_678, retro_mluc_722, retro_mluc_830,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Sarcophilus harrisii	ENSSHAG00000005486	1 retrocopy	retro_shar_549,
Tarsius syrichta	ENSTSYG00000008569	8 retrocopies	retro_tsyr_1048, retro_tsyr_116, retro_tsyr_1521, retro_tsyr_2090, retro_tsyr_347, retro_tsyr_535 , retro_tsyr_757, retro_tsyr_87,