RetrogeneDB ID: retro_tsyr_293

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_7350:175..895(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000008497
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KCTD18
• Ensembl ID: ENSTSYG00000008420
• Aliases: None
• Description: potassium channel tetramerization domain containing 18 [Source:HGNC Symbol;Acc:26446]

Sequence

>retro_tsyr_293
AAGCATTTTTTTTAAAAAGAGGCAGGAAATAACGTCCAGTACATCTGGAGCTGTTATTCAGCAGCAGAGTTGAAGATGAT
GGACGCCTTCGATGCTTGGGAAGGAAAAGGTGTGAGCTACTGGCAGGTGCCCCACGAGCTGATCGAGTGCTGGACTCTGG
AGGAGTGGCTGCTGCTGGGAAACCTGCGCCACATGGCCCCTGTCCGGAAGAGGCGCCTGGTCATGTTCCCTGAAGAGGAA
GATGTGAACTGTAAGCCTGGTCCTAGGCCCATCCAGTTTTGGGGCCCTTCCACAAGTACCCAGATTAAAGTCAGGAACTC
GGCCTTGGTCAGGGTGTCCCTGGCGACTGCCGCCTTATCCTCGGCTCGGGTGAACACACAACAGTGTCACAGTGGCAGTG
GTGGAATAGCAGCTTCATGTCGGGTAACTTCCAAGGCCGTGTCCCTGGGAAGTACGGGGACCCCAGTACTCACCCAGGCA
TCCCTTGGGGCTGGGGGCGCTGAAAATGGAGGTGCACATTCACCTGCAGCAAAGGTGCTGCTCCCCAACAGGAAGGCCAC
ACCCCACCGTGAGATAAAGCTCAAGAGGACTCCTCCACGTGCTGCAGTGCCCTCCCGGCCCACACCCCCGGTGGGCCATG
CCTGTGCCCTGGAGCCACCTCCCCTCCTCGAGTCCTCCAGCACTCAAGGAGTGCAGACTGAGCACAGGACTGACCAGGAC

Alignment

ORF - retro_tsyr_293 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.1 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSIFKREAGNNVQYIWSYYSAAELKKMMDAFDAWEGKGVSYWRVPHELIECWTLEERPLLGSLRHMAPVR
          K.....EAGNNVQYIWS.YSAAELK.MMDAFDAWEGKGVSYW.VPHELIECWTLEE..LLG.LRHMAPVR
Retrocopy KXXXXKEAGNNVQYIWSCYSAAELK-MMDAFDAWEGKGVSYWQVPHELIECWTLEEWLLLGNLRHMAPVR

Parental  KRRLVTFPEEAEDVNCKPGPKPIRFLGPSTSTQIKVKNSASVRVSPTTAASSSARVTMRQCHSSSSGMAA
          KRRLV.FPEE.EDVNCKPGP.PI.F.GPSTSTQIKV.NSA.VRVS..TAA.SSARV...QCHS.S.G.AA
Retrocopy KRRLVMFPEE-EDVNCKPGPRPIQFWGPSTSTQIKVRNSALVRVSLATAALSSARVNTQQCHSGSGGIAA

Parental  PCLVTSKAVSLGGMATSALTQASLGAGGAENGGAHPPAVKVLLPDRKATPHRVIKLKRTPLRAVVPSRPA
          .C.VTSKAVSLG...T..LTQASLGAGGAENGGAH.PA.KVLLP.RKATPHR.IKLKRTP.RA.VPSRP.
Retrocopy SCRVTSKAVSLGSTGTPVLTQASLGAGGAENGGAHSPAAKVLLPNRKATPHREIKLKRTPPRAAVPSRPT

Parental  ATGSQDCTPEPLPLLEASSSQGVQTEHGTDQD
          ......C..EP.PLLE.SS.QGVQTEH.TDQD
Retrocopy PPVGHACALEPPPLLESSSTQGVQTEHRTDQD

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_293 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000031173	2 retrocopies	retro_cjac_1956, retro_cjac_3169,
Otolemur garnettii	ENSOGAG00000012335	1 retrocopy	retro_ogar_3268,
Tarsius syrichta	ENSTSYG00000008420	2 retrocopies	retro_tsyr_293 , retro_tsyr_896,