RetrogeneDB ID: retro_tsyr_834

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_21184:17393..18361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNI
• Ensembl ID: ENSTSYG00000009907
• Aliases: None
• Description: cyclin I [Source:HGNC Symbol;Acc:1595]

Sequence

>retro_tsyr_834
CTGACCAAACTCAGAAACTAATTCACCCTTTACCCTGAAACACTTGCTCTGGCTAGCAGTCTTTTGGACAAGTTTTTAGC
TGTTGTAAAGCCCCCCCCCCCCGCCCCCAAATACCTGAGCTGTATTGCAATGAGCTGTTTTTGCCTAGTTGCCAAGATAG
TTGAGGAAAATGAGAGAATTCCATTACTGAAGGTGTTGACAAGAGGCAGTTTCTGTGGATGTTTCTATTCTGAAATTCTG
AGAATGGAGAGAATTATTCTGGATAAGTTGAATTAGAATCTCCACACAAACACACCTTTGAAATTTCTTCACATTTTCCA
TGACATTACAGTGTCCATGAGGCCTCAGTTACTTTTCAATTTGCCCAAATGGAGCCTGTCTCAACATTTGGAGGTCCTTA
CCAAGCAAATACTTCACTGTATGGCCTGCAACCAACTTCTGCAATTCAAAGGAGCCAGGCTTGCTCTGACCATGGATAGC
CTGGAAATGGAGAAACTCATTTCTGATTGGTTTTCTCTTACAATGAACTCCTTCAGTAAGCATAAATGGGTAACTCCTAC
TTGATCTGATGTCATGAGCTTGTGGCACATCACCCTTCTACTTTGCAGTCTTTCCTGCCTGTAAATCTCATTTTTGCCAA
CCATCCCCTCAAGCACACCGTGGTGACCTGTGACAAATGAGTCTTCCGATTATATTCCTTCTGTGTCCTAGGCCCAGATT
TCTCAAAGGACAGCAGCAAACCAGAAGTGCCAGTCAGAGAGGCATAGCAGTCTTCTACTACCTTCTCCCTGTTGCCAATG
GGTGCAGGTATACCTCTGCTAAACACCAAGGAAGGGAAATGGAAGTGATGACTTCTGTGGTCAAATCAAATGGCTCCATA
GTGAAGATACTGCTTCAGAAGTTGTGGGTTCTGTGTGTGACACTGATTTATCAAGACAATGGAACATGCTTCTCCATGTC
CACCTTTG

Alignment

ORF - retro_tsyr_834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 84.88 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LAKLKYQFNLYPETFALASSLLDRFLATVKAHP---KYLSCIAISCFFLAAKTVEEDERIPVLKVLARDS
          L.KL...F.LYPET.ALASSLLD.FLA.VK......KYLSCIA.SCF.L.AK.VEE.ERIP.LKVL.R.S
Retrocopy LTKLRN*FTLYPETLALASSLLDKFLAVVKXXXXXXKYLSCIAMSCFCLVAKIVEENERIPLLKVLTRGS

Parental  FCGCSSSEILRMERIILDKLNWDLHTATPLDFLHIFHAIAVSTRPQLLFSLPKLSPSQHLTVLTKQLLHC
          FCGC..SEILRMERIILDKLN..LHT.TPL.FLHIFH.I.VS.RPQLLF.LPK.S.SQHL.VLTKQ.LHC
Retrocopy FCGCFYSEILRMERIILDKLN*NLHTNTPLKFLHIFHDITVSMRPQLLFNLPKWSLSQHLEVLTKQILHC

Parental  MACNQLLQFKGSMLALAMVSLEMEKLIPDWLPLTI-ELLQKAQMDSSQLIHCRELVAHHLSTLQSALPLN
          MACNQLLQFKG..LAL.M.SLEMEKLI.DW..LT..ELLQ.A.M..S.LI.C.ELVAHH.STLQS.LP.N
Retrocopy MACNQLLQFKGARLALTMDSLEMEKLISDWFSLTM<ELLQ*A*MGNSYLI*CHELVAHHPSTLQSFLPVN

Parental  SVYVYRPLKHTLVTWDKGVFRSHPSSV-PGPDFSKDNSKPE-VPVRGTAAFCHHLPAASGCKYAFTKRKV
          ......PLKHT.VT.DK.VFR.....V.P.P.F.K..........RG.A.F...LP.A.GC.Y...K...
Retrocopy LIFANHPLKHTVVTCDK*VFRLYSFCV<PRPRFLKGQQQTRSASQRGIAVFYYLLPVANGCRYTSAKHQG

Parental  EEMEV-DDFYDGIKRLYNEENASENVGSVCGTDLSRQEG-HASPCPPL
          .EMEV.DDF...IK.L..E..ASE.VGSVC.TDLSRQ...HASPCPPL
Retrocopy REMEV<DDFCGQIKWLHSEDTASEVVGSVCDTDLSRQWN<HASPCPPL

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_834 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Echinops telfairi	ENSETEG00000000952	1 retrocopy	retro_etel_1137,
Loxodonta africana	ENSLAFG00000029218	1 retrocopy	retro_lafr_295,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730,
Tarsius syrichta	ENSTSYG00000009907	1 retrocopy	retro_tsyr_834 ,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197,