RetrogeneDB ID: retro_tsyr_1648

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_53097:4176..4644(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSTSYG00000006848
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_tsyr_1648
GATGCTGAGGATGCAATTTATGGAAGGAATGATTATGATTATGGTCAGTGTCGGCTTCGTGTGAAGTTCCCCAGGACTTA
TGGAAGTTGGGGTGGGTGGCCCTGAGGTGGGAGGAATGGGACTCCTACAAGAAGATCTGATTTCCAAGTTGTTTCAGGAC
TTCCTCCATCAGGCAGCTGGCAAAACCTGAAGGATCACATGCGAGAAGCTGGGGCTGTCTGTTATACAGATGTGCAGAAG
GATGGAATGGGGATGGTTGAGTATCCCAGAAAAGACATGGAATATGCCCTGTGTAAACTGGATGACAACAAATTCTGCTC
TCATGAGAGTGAAACTTCCTACATCCGAGTTTATCCTGAGAGAAGCACCAGCTATGGCTACTCACGGTCCGGGTCTAGGT
CAAGGGGCCATGATTCTCCATACCAAGGCAGGGGTTCCCCACACTACTTCTCTCCTTTCAGGCACTTA

Alignment

ORF - retro_tsyr_1648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.28 %
• Parental protein coverage: 72.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAEDAIYGRNGYDYGQCRLRVEFPRTYGSRGGWPRGGRNGPPTRRSDFRVLVSGLPPSGSWQDLKDHMRE
          DAEDAIYGRN.YDYGQCRLRV.FPRTYGS.GGWP.GGRNG.PTRRSDF.V.VSGLPPSGSWQ.LKDHMRE
Retrocopy DAEDAIYGRNDYDYGQCRLRVKFPRTYGSWGGWP*GGRNGTPTRRSDFQV-VSGLPPSGSWQNLKDHMRE

Parental  AGDVCYADVQKDGMGMVVYPRKEDMEYALQILGDNKFRSHEECETF---YPEKCTSYGYSRSWSGSRGHD
          AG.VCY.DVQKDGMGMV.YPRK.DMEYAL..L.DNKF.SHE........YPE..TSYGYSRS.S.SRGHD
Retrocopy AGAVCYTDVQKDGMGMVEYPRK-DMEYALCKLDDNKFCSHESETSYIRVYPERSTSYGYSRSGSRSRGHD

Parental  SPYQGRGSPHYFSPFRHL
          SPYQGRGSPHYFSPFRHL
Retrocopy SPYQGRGSPHYFSPFRHL

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_1648 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648 , retro_tsyr_585, retro_tsyr_891,
Tarsius syrichta	ENSTSYG00000013498	3 retrocopies	retro_tsyr_1867, retro_tsyr_2163, retro_tsyr_848,