RetrogeneDB ID: retro_tsyr_1184

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_340453:492..893(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSTSYG00000010706
• Aliases: None
• Description: replication protein A2, 32kDa [Source:HGNC Symbol;Acc:10290]

Sequence

>retro_tsyr_1184
AACAAAAAGAGCCTGGTAGCCTTTAATATCATAACCCTGGAGGATATGAATGAGTTTGCCACACATATTCTGGAAGTAGT
CAATGCACACATGACATTGAGCAAATCTAATAGCCAGCCCTCAGCAGGAAGAGTACCTATCAGCAATCCAGGAATTCATG
AAGCAGGGAACTTTGATGGGATAGCTTCATGCCAGCAAATGGCCTCACTGTGGCCCAAAACCAGGTGGGTGAATTTGATT
AAGGCTTGCCCAAGTCCTGAAGAATTGAACTTTCAGGATCTCAAGAACCAGCTCTCACACATGACTATGACTCCACTCAG
GCAGGCTGTGGATTTTCTTAACAATGAAAGATAAGTTACTCTACTGTGAATGATAATCATTTTAAATCTACAGATACAGA
A

Alignment

ORF - retro_tsyr_1184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.26 %
• Parental protein coverage: 57.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NKKSLVAFKIMPLEDMNEFTTHMLEVVNAHMVLNKSNSQPSAGRAPVNNL-MSEAGSFSG-NSFIPANGL
          NKKSLVAF.I..LEDMNEF.TH.LEVVNAHM.L.KSNSQPSAGR.P..N....EAG.F.G..SF.PANGL
Retrocopy NKKSLVAFNIITLEDMNEFATHILEVVNAHMTLSKSNSQPSAGRVPISNPGIHEAGNFDG<DSFMPANGL

Parental  TVAQNQV-LNLIKACPRPEGLNFQDLRNQLKHMTVPSIKQAVDFLSNEGHI-YSTVDDDHFKSTDAE
          TVAQNQV..NLIKACP.PE.LNFQDL.NQL.HMT.....QAVDFL.NE....YSTV.D.HFKSTD.E
Retrocopy TVAQNQV>VNLIKACPSPEELNFQDLKNQLSHMTMTPLRQAVDFLNNER*V<YSTVNDNHFKSTDTE

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_1184 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tarsius syrichta	ENSTSYG00000010706	2 retrocopies	retro_tsyr_1184 , retro_tsyr_1806,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,