RetrogeneDB ID: retro_tsyr_15

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_32060:3..672(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000002499
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000009555
• Aliases: None
• Description: None

Sequence

>retro_tsyr_15
TCGAGCTCGCCTCGGAGCGGCGGCGGGGAAATGCACGGGCGGCTCCCCGCCGCGCGCGGGCGAGACGGCTACGCGGGCCC
GCTGCGCCGGGAGCCGCCGCCCCCGCGCCGCGACCCCTACCTGGGCCCGAGGGAGGAGGGCTACTCGCCCAGAGATAGCT
ACTCGAGCCGCGACTACCGCGACCCCCGGGATTTCGCCCCCTCGCCCAGAGAGTACACCTACCGCGATTACGGCCACCCC
GGTGCCCGGGACGACTGTCCCTCGAGAGGCTACGGCGACCGCGACGGCTACGGGGGTCGCGACCGTGACTACACGGATCA
CCCGAGCGGAGGCTCCTACCGAGATCTCTTTGAGAGCTACGGGGACCCGCGCGGCGCCCCGCCGGCGCGGGGGCCCCCGC
CATCTTACGGAGGAGGAGGAGGCGGCCGCTACGAGGAGTACCGCGGCTGCTCGCCCGACGCCTACAGCGGCGGCCGCGAC
AGTTACGGCAGCGGCCGCAGTGACCGCTACTCGAGGGGCCGAGAGCGGGTGGGCAGACCGGATCGCGGGCTCCCTCCGTC
CATGGAAAGGGGGTACGCGCCCCCGCGTGATTCCTACAGCCGGTCGGGCCGCCGAGTGCCCCGGGGCGGAGGCCGCCTGG
AAAGAGGGGGAGGCAGGAGCAGATACTGA

Alignment

ORF - retro_tsyr_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.54 %
• Parental protein coverage: 57.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGPVRSSSGWGGRAPVSRGRDSYGGPPRREPLPFRRDVYLSPRDDGYSTKDSYSSRDYPSSRDTRDYAPP
          S.P........GR.P..RGRD.Y.GP.RREP.P.RRD.YL.PR..GYS..DSYSSRDY...RD.RD.AP.
Retrocopy SSPRSGGGEMHGRLPAARGRDGYAGPLRREPPPPRRDPYLGPREEGYSPRDSYSSRDY---RDPRDFAPS

Parental  PRDYTYRDYGHSSSRDDYPSRGYSDRDGYG-RDRDYSDHPSGGSYRDSYESYGNSRSAPPTRGPPPSYGG
          PR.YTYRDYGH...RDD.PSRGY.DRDGYG.RDRDY.DHPSGGSYRD..ESYG..R.APP.RGPPPSYGG
Retrocopy PREYTYRDYGHPGARDDCPSRGYGDRDGYGGRDRDYTDHPSGGSYRDLFESYGDPRGAPPARGPPPSYGG

Parental  SS--RYDDYSS-SRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLPPSMERGYPPPRDSYSSSSRGAPR
          ....RY..Y...S.D.Y.G.RDSY.S.RSD.YS.GR.RVGR..RGLPPSMERGY.PPRDSYS.S.R..PR
Retrocopy GGGGRYEEYRGCSPDAYSGGRDSYGSGRSDRYSRGRERVGRPDRGLPPSMERGYAPPRDSYSRSGRRVPR

Parental  GGGRGGSRSDRGGGRSRY
          GGG....R..RGGGRSRY
Retrocopy GGG----RLERGGGRSRY

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_15 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 20 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15 ,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,