RetrogeneDB ID: retro_tsyr_1913

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_6637:31268..31786(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCAN1
• Ensembl ID: ENSTSYG00000006972
• Aliases: None
• Description: regulator of calcineurin 1 [Source:HGNC Symbol;Acc:3040]

Sequence

>retro_tsyr_1913
ATGTTGGTGGACAGCCTGTGCCAGGCCACATTTGAGTCCCCTTTGAGGACATAGGAAAAGGACATCACCTTTCAGTATTT
TAAAAGCTTTAAATGAGTTAGAATAAACTTCAGTAACCCCTTTTCTGCAGCAGCTGCCGGACTCCAGCTACTTAAGACTG
AGTTTCTTAGAAAGGAAATGAAGTTCTGCTCAGTTTTTACACATAGGAAGCTCACACCTGGCTCCGCCAAGTCCAAACAG
GCGGTTTCTGATTGCTCCTCCCACCTCCTGCCAGTTGGTTGGAAACAAGAGGAAGACGCTACCCTAATCATAAAGTATGA
TCTTTTTAATGCTACCTCCAAGTTGAGGTCAGAGGAAAAGTATGAATTGTATTCAGAGGCCAACAGCACTCCCACTGTGG
TGGGCCATGTGTGCAAGAGCATTCAAGAGAAAGCGAAAGAAGAGATGGAGAGAATGAAGAGACCCAAGCCAAAATTATCT
AGACCAGAAGGCCAGAGTACTCACCTATCCACCTCAAC

Alignment

ORF - retro_tsyr_1913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.6 %
• Parental protein coverage: 70.97 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFVDGLNRAKFESLFRTYDKDITFQYFKSFKRVRINFSNPFSAADARLQLHKTE-FLGKEMKLYFAQTLH
          ..VD.L..A.FES..RT..KDITFQYFKSFK.VRINFSNPFSAA.A.LQL.KTE.FL..E.K...AQ.LH
Retrocopy MLVDSLCQATFESPLRT*EKDITFQYFKSFK*VRINFSNPFSAAAAGLQLLKTE>FL--ERK*SSAQFLH

Parental  IGSPHLAPPNPDKQFLISPPASP-PVGWKQVEDATPVINYDLLYAISKLGPGEKYELHAATDTTPSVVVH
          IGS.HLAPP.P...FLI.PP.S..PVGWKQ.EDAT..I.YDL..A.SKL...EKYEL......TP.VV.H
Retrocopy IGSSHLAPPSPNRRFLIAPPTSC<PVGWKQEEDATLIIKYDLFNATSKLRSEEKYELYSEANSTPTVVGH

Parental  VCESDQEKEEEEEMERMKRPKP-KIIQTRRPEYTPIHLS
          VC.S.QEK...EEMERMKRPKP.KII.TRRPEY.PIHL.
Retrocopy VCKSIQEK-AKEEMERMKRPKP<KII*TRRPEYSPIHLN

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_1913 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002838	2 retrocopies	retro_cjac_4016, retro_cjac_437,
Cavia porcellus	ENSCPOG00000010683	1 retrocopy	retro_cpor_1267,
Tarsius syrichta	ENSTSYG00000006972	1 retrocopy	retro_tsyr_1913 ,