RetrogeneDB ID: retro_tsyr_1609

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_510890:421..829(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSTSYG00000002837
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_tsyr_1609
GAAGACTATGACCGTCTGAGGCCTTTATCTTACCCGATGACCAATGTCTTCCTTATATGCTTCTCAGTGGTAAATCCAGC
TTCATTTCAAAACGTGAAAGAGAGTGGGTACCGGAACTTAAGGAATATGCACCAAATATTCCCTTTTTATTAATAGGAAC
TCAGATTGGTCTCCGGGATGACCCCAAAACTTTAGCAAGACTGAATGATATGAAAGAAAGGCCTATATGTGTGGAGCAAG
GACAGAAACTAGTGAAAGAGATAGGAGCATGCTGATATGAGGAACGTTCAACTTTAACCCAGAAGGGATTGAAGTCTGTT
TTTGATGATGCTATCATAGCCATTTAACTCCAAAGAAACACACAGTAAAAAAAGAATAGGATCAAGATGTATAAACTGTT
GTTTGATT

Alignment

ORF - retro_tsyr_1609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKE-EWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARLN
          EDYDRLRPLSYPMT.VFLICFSVVNPASFQNVKE.EWVPELKEYAPN.PFLLIGTQI.LRDDPKTLARLN
Retrocopy EDYDRLRPLSYPMTNVFLICFSVVNPASFQNVKE<EWVPELKEYAPNIPFLLIGTQIGLRDDPKTLARLN

Parental  DMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAI-LTPKKHTV-KKRIGSRCINCCLI
          DMKE.PICVEQGQKL.KEIGAC.Y.E.S.LTQKGLK.VFD.AIIAI.LTPKKHTV.KKRIGSRCINCCLI
Retrocopy DMKERPICVEQGQKLVKEIGAC*YEERSTLTQKGLKSVFDDAIIAI<LTPKKHTV<KKRIGSRCINCCLI

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_1609 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000000679	11 retrocopies	retro_tsyr_1575, retro_tsyr_1597, retro_tsyr_1854, retro_tsyr_1976, retro_tsyr_2048, retro_tsyr_2098, retro_tsyr_352, retro_tsyr_387, retro_tsyr_539, retro_tsyr_66, retro_tsyr_963,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609 ,