RetrogeneDB ID: retro_tsyr_1543

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_484617:271..1105(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSTF1
• Ensembl ID: ENSTSYG00000003181
• Aliases: None
• Description: cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa [Source:HGNC Symbol;Acc:2483]

Sequence

>retro_tsyr_1543
ATGAACCGCACACAGAATATGGAAAACCACCCAGTGATTCAAACTCTTTATGACCACGTGGATGAAGTCATATGTCTCGC
TCTCCACCCAACAGAACAGATCCTGGCTTCTGGGTCAAGGGATTATACTCTTAAATTATTTGATTATTCCAAACCATCCA
CAGAAAGAGCCTTCAAATATATCCTGGAGGCTGAAATGCTACGCTCCGTCTCTTTTCATCCTTCTGGAGACTTTATACTT
GTTGGAACTCAGCATCCTACTCTTCACCTTTATGACATCAACACCTTTCAGTGTTTTGCCTCTTGCAATCCTCAAGATCA
ACACCCTGATGCAATATGTTCCATGAATTACAATCCTGGTGCCAATATGTATGTAACTGAAAGCAAGGACGGCTGCATCA
AATTATGGGATGGTGTTTCAAATCGATGCTTCACAACTTTTGAGAAAGCACATGACGGTGCTAGAGTTTGTTCTGCAATT
TTTTCCAAAAATTCTAAATATATTCTCTCAAGTGGAAAAGACTCTGTAGCTAAACTTTGGGAAATATCAACAGGAAGAAC
ACTGGTCAGATACATGGGCGCGGGTCTGAGTGGACGGCAGGTGCATCGGACACAGGCCGTGTTTAACCACACCAAGGACT
ATGTGTTACTGCCTGATGAAAGGACAATCAGTCTGTGCTGCTAGGACTCAAGGATGGCTGAGCGAAGAAACCTGCTCTCC
TTGGGGCACAACAACATCGTGCGCTGCATCGTGCACTCGCCCACCAACCCTGGATTCATGATGTGCAGCGATGACTTCAG
AGCACGGTTTTGGTACCGGAGGTCAACCATCGAC

Alignment

ORF - retro_tsyr_1543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 64.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNETAQQNMENHPVIRTLYDHVDEVTCLAFHPTEQILASGSRDYTLKLD--SKPSAKKAFKYIQEAEMLR
          MN.T..QNMENHPVI.TLYDHVDEV.CLA.HPTEQILASGSRDYTLKL...SKPS...AFKYI.EAEMLR
Retrocopy MNRT--QNMENHPVIQTLYDHVDEVICLALHPTEQILASGSRDYTLKLFDYSKPSTERAFKYILEAEMLR

Parental  SISFHPSGDFILVGTQHPTLRLYDINTFQCFVSCNPQDQHTDAICSVNYNPSANMYVTGSKDGCIKLWDG
          S.SFHPSGDFILVGTQHPTL.LYDINTFQCF.SCNPQDQH.DAICS.NYNP.ANMYVT.SKDGCIKLWDG
Retrocopy SVSFHPSGDFILVGTQHPTLHLYDINTFQCFASCNPQDQHPDAICSMNYNPGANMYVTESKDGCIKLWDG

Parental  VSNRCITTFEKAHDGAEVCSAIFSKNSKYILSSGKDSVAKLWEISTGRTLVRYTGAGLSGRQVHRTQAVF
          VSNRC.TTFEKAHDGA.VCSAIFSKNSKYILSSGKDSVAKLWEISTGRTLVRY.GAGLSGRQVHRTQAVF
Retrocopy VSNRCFTTFEKAHDGARVCSAIFSKNSKYILSSGKDSVAKLWEISTGRTLVRYMGAGLSGRQVHRTQAVF

Parental  NHTEDYVLLPDERTISLCCWDSRTAERRNLLSLGHNNIVRCIVHSPTNPGFMTCSDDFRARFWYRRSTTD
          NHT.DYVLLPDERTISLCC.DSR.AERRNLLSLGHNNIVRCIVHSPTNPGFM.CSDDFRARFWYRRST.D
Retrocopy NHTKDYVLLPDERTISLCC*DSRMAERRNLLSLGHNNIVRCIVHSPTNPGFMMCSDDFRARFWYRRSTID

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_1543 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011281	2 retrocopies	retro_cjac_3572, retro_cjac_4012,
Tarsius syrichta	ENSTSYG00000003181	2 retrocopies	retro_tsyr_1543 , retro_tsyr_32,