RetrogeneDB ID: retro_tsyr_1572

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_49405:2284..2867(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf29
• Ensembl ID: ENSTSYG00000014665
• Aliases: None
• Description: chromosome 12 open reading frame 29 [Source:HGNC Symbol;Acc:25322]

Sequence

>retro_tsyr_1572
GATCCAGTGCCTGATGAAAATGGACACATCCCTGGTTGGGTACAGTAGAGAAAAAGAACAAACAGTATTGCTGGCATTCC
TCTGTCATTAATTATGAATTTGAAATTGCCCTGGTGATAAAGCATCATCCTGATGATCCTGGAGTTTTGGAAATTAGTGC
AGTGCCACTGTCATATCTCTTAGAACAGACCCTGGAGCTCATAGGAACAAATATCAATGGAAATCCATATGGGTTAGGAA
GCAAGAAGCATCCATTACATCTTCTTATACCACATGGAGCATTTCAAATAAGAACTCTGCCTACATTGAAGCACAATGAT
GTCTTTTACTGGTTTGAAGGTTGCAGAGAGGGTAAAATTGAAGAAATAGTCTGGCATTGCAGTGATGGCTGTTTAATTAA
GGTCCATCACCATCATCTTGGTTTATGCTGGCCAATTCCAAATACTTACATGAATTCAAAACCAGTTATTATCAACATGA
ACTTGAACAAATATGACTATGTCTTTGATACTGTTTGTTTAATCATTTTTTTAAAAAAGATAATCAGAAATTTGGTAGGC
TCAAAGACATAATGCTTGATGTA

Alignment

ORF - retro_tsyr_1572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.9 %
• Parental protein coverage: 59.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NPVPDENGHIPGWVP-VEKNNKQYCWHSSVINYEFEIALVLKHHPDDPGVLEISAVPLSDLLEQTLELIG
          .PVPDENGHIPGWV..VEK.NKQYCWHSSVINYEFEIALV.KHHPDDPGVLEISAVPLS.LLEQTLELIG
Retrocopy DPVPDENGHIPGWVQ<VEKKNKQYCWHSSVINYEFEIALVIKHHPDDPGVLEISAVPLSYLLEQTLELIG

Parental  TNINGNPYGLGSKKHPLHFLIPHGAFQIRTLPTLKHNDLLSWFEGCREGKIEGIVWHCSDGCLIKVHRHH
          TNINGNPYGLGSKKHPLH.LIPHGAFQIRTLPTLKHND...WFEGCREGKIE.IVWHCSDGCLIKVH.HH
Retrocopy TNINGNPYGLGSKKHPLHLLIPHGAFQIRTLPTLKHNDVFYWFEGCREGKIEEIVWHCSDGCLIKVHHHH

Parental  LGLCWPIPDTYMNSKPVIINMNLNKYDYVFDTKCLFNHFLK-IDNQKFGRLKDIKLDV
          LGLCWPIP.TYMNSKPVIINMNLNKYDYVFDT.CL...FLK..DNQKFGRLKDI.LDV
Retrocopy LGLCWPIPNTYMNSKPVIINMNLNKYDYVFDTVCLI-IFLK<KDNQKFGRLKDIMLDV

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_1572 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011011	1 retrocopy	retro_chof_1262,
Homo sapiens	ENSG00000133641	1 retrocopy	retro_hsap_3984,
Gorilla gorilla	ENSGGOG00000005986	1 retrocopy	retro_ggor_2674,
Loxodonta africana	ENSLAFG00000013286	1 retrocopy	retro_lafr_706,
Macaca mulatta	ENSMMUG00000015860	1 retrocopy	retro_mmul_715,
Nomascus leucogenys	ENSNLEG00000005396	1 retrocopy	retro_nleu_1905,
Pan troglodytes	ENSPTRG00000005277	1 retrocopy	retro_ptro_2704,
Rattus norvegicus	ENSRNOG00000006973	1 retrocopy	retro_rnor_1625,
Tupaia belangeri	ENSTBEG00000005256	1 retrocopy	retro_tbel_94,
Tarsius syrichta	ENSTSYG00000014665	1 retrocopy	retro_tsyr_1572 ,