RetrogeneDB ID: retro_tsyr_660

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_162207:537..1034(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR3
• Ensembl ID: ENSTSYG00000010578
• Aliases: None
• Description: signal sequence receptor, gamma (translocon-associated protein gamma) [Source:HGNC Symbol;Acc:11325]

Sequence

>retro_tsyr_660
GAGGACCTCAGCCGCAAACTCTCAGCCAAGTCATCTGCGCTCTTCTTTGGTAATGCGTTCATCGTGTCCGCCATCCCCAT
CTTGGCGAATATGGCATATGGATCTTATTCAATCTGCTGTTCTCTATAGCATGCTGGTCCTAGTAAGCACATGTTTGGTA
GCCTTTGCAGACAAGAATGTAAAATTTGTTCTCAAGCACAAAGTGGCACAGAAGAGTGAGGATGCTATTTCCAAAGAAGT
GACTTGGAAACTTTCTGAAGCTGATAATTGAAAGATGTCACGGAAGGAGAAAGATGAAAGAATCTTGTGGAAGAAGAATG
AAGTTGCTGATTATGAAGTTACAACATTTTCCATCTTCTACAACAACACTCTGTTCTTGGTCTTGGTCATTGTGGCTTTC
TTCTTTATATTGAAGAACTTCATTCCTACAAGTGAACTACACTTTGTTCATAAGTGCATCATCAGGACTCATTGCCCTCC
TGTCTGCTGGCTCCAAG

Alignment

ORF - retro_tsyr_660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 89.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QDFSRNLSAKSSALFFGNAFIVSAIPI-WLYWRIWHMDLIQSAVLYSVMTLVSTYLVAFAYKNVKFVLKH
          .D.SR.LSAKSSALFFGNAFIVSAIPI.W..W...HMDLIQSAVLYS...LVST.LVAFA.KNVKFVLKH
Retrocopy EDLSRKLSAKSSALFFGNAFIVSAIPI>WRIW---HMDLIQSAVLYSMLVLVSTCLVAFADKNVKFVLKH

Parental  KVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFYNNTLFLVLVIVASFFI
          KVAQK.EDA.SKEVT.KLSEADN.KMSRKEKDERILWKKNEVADYE.TTFSIFYNNTLFLVLVIVA.FFI
Retrocopy KVAQKSEDAISKEVTWKLSEADN*KMSRKEKDERILWKKNEVADYEVTTFSIFYNNTLFLVLVIVAFFFI

Parental  LKNFNPT-VNYILSISASSGLIALLSTGSK
          LKNF.PT.VNY.L.ISASSGLIALLS.GSK
Retrocopy LKNFIPT>VNYTLFISASSGLIALLSAGSK

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_660 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003125	1 retrocopy	retro_amel_832,
Canis familiaris	ENSCAFG00000008870	5 retrocopies	retro_cfam_1296, retro_cfam_1370, retro_cfam_1924, retro_cfam_2029, retro_cfam_2041,
Choloepus hoffmanni	ENSCHOG00000001517	1 retrocopy	retro_chof_29,
Callithrix jacchus	ENSCJAG00000004643	4 retrocopies	retro_cjac_1059, retro_cjac_1503, retro_cjac_2369, retro_cjac_3213,
Cavia porcellus	ENSCPOG00000005898	2 retrocopies	retro_cpor_1243, retro_cpor_826,
Dasypus novemcinctus	ENSDNOG00000000752	2 retrocopies	retro_dnov_1922, retro_dnov_632,
Homo sapiens	ENSG00000114850	1 retrocopy	retro_hsap_173,
Gorilla gorilla	ENSGGOG00000024038	1 retrocopy	retro_ggor_255,
Myotis lucifugus	ENSMLUG00000015478	3 retrocopies	retro_mluc_1624, retro_mluc_1728, retro_mluc_2146,
Macaca mulatta	ENSMMUG00000016970	1 retrocopy	retro_mmul_383,
Otolemur garnettii	ENSOGAG00000010589	2 retrocopies	retro_ogar_2089, retro_ogar_3483,
Pongo abelii	ENSPPYG00000014233	1 retrocopy	retro_pabe_456,
Pan troglodytes	ENSPTRG00000015560	1 retrocopy	retro_ptro_163,
Tarsius syrichta	ENSTSYG00000010578	1 retrocopy	retro_tsyr_660 ,