RetrogeneDB ID: retro_tsyr_1342

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_4053:7745..8184(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP18
• Ensembl ID: ENSTSYG00000005454
• Aliases: None
• Description: Sin3A-associated protein, 18kDa [Source:HGNC Symbol;Acc:10530]

Sequence

>retro_tsyr_1342
GTCATCCAGGAGGAGATCAAGAAGGAGTCGAAGAAACCGATCCACCCAAGAAGACATGCCCACTGCTGCTACGTGTCCTT
ACCACCCCAACGGCTGCCACCACCACATGATGAGTTCTCCCGCAGGAACGTGCCGTCCAGCGAGCTGCAGATCTGCATCT
GGATAGATGCAACCTTGAAAGAACTGCCTAGTTTAGTGAAAGAAATCTACCCAGAAGCTAGAAAGAAGGGCACACACTTC
AATTTTGCCATCGTTTTCACCAATGTCAAAAGACCTGGCTACCGAGTTAAGGAGATCGGCAGCACCATGTCTGGCAGAAA
GGGGACTGATGGCTCTATGACGCCACAGTCGCAGAAGTTTCAGATACCAAATTATTTGGACATGGTGTTCACCCCCCCAA
ACCCAGGTACCACCCCACTTGGGGCACATGAGACCATAT

Alignment

ORF - retro_tsyr_1342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 96.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VTQEEIKKEPEKPIDR-EKTCPLLLRVFTTN-NGRHHRM-DEFSRGNVPSSELQIYTWMDATLKELTSLV
          V.QEEIKKE..KPI....KTCPLLLRV.TT..NG.HH.M.DEFSR.NVPSSELQI..W.DATLKEL.SLV
Retrocopy VIQEEIKKESKKPIHP<KKTCPLLLRVLTTP<NGCHHHM<DEFSRRNVPSSELQICIWIDATLKELPSLV

Parental  KEVYPEARKKGTHFNFAIVFTDVKRPGYRVKEIGSTMSGRKGTDDSMTLQSQKFQIGDYLDIAITPPN-R
          KE.YPEARKKGTHFNFAIVFT.VKRPGYRVKEIGSTMSGRKGTD.SMT.QSQKFQI..YLD...TPPN..
Retrocopy KEIYPEARKKGTHFNFAIVFTNVKRPGYRVKEIGSTMSGRKGTDGSMTPQSQKFQIPNYLDMVFTPPN>Q

Parental  APPTSGRMRPY
          .PP..G.MRPY
Retrocopy VPPHLGHMRPY

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_1342 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 6 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000006309	1 retrocopy	retro_eeur_674,
Mustela putorius furo	ENSMPUG00000000607	1 retrocopy	retro_mputfur_35,
Mus musculus	ENSMUSG00000021963	1 retrocopy	retro_mmus_82,
Pteropus vampyrus	ENSPVAG00000016315	2 retrocopies	retro_pvam_1246, retro_pvam_43,
Rattus norvegicus	ENSRNOG00000010732	1 retrocopy	retro_rnor_163,
Tarsius syrichta	ENSTSYG00000005454	22 retrocopies	retro_tsyr_1018, retro_tsyr_1117, retro_tsyr_1225, retro_tsyr_1342 , retro_tsyr_1439, retro_tsyr_1490, retro_tsyr_1578, retro_tsyr_1708, retro_tsyr_1767, retro_tsyr_1851, retro_tsyr_1938, retro_tsyr_2118, retro_tsyr_2179, retro_tsyr_398, retro_tsyr_451, retro_tsyr_563, retro_tsyr_826, retro_tsyr_837, retro_tsyr_886, retro_tsyr_892, retro_tsyr_901, retro_tsyr_967,