RetrogeneDB ID: retro_tsyr_257

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_6531:5270..6078(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf43
• Ensembl ID: ENSTSYG00000009317
• Aliases: None
• Description: chromosome 12 open reading frame 43 [Source:HGNC Symbol;Acc:25719]

Sequence

>retro_tsyr_257
ATGGTGGCGCTCAATGGTGCCACGAGCGATTCAGAAAGCAGTAGCGGCAGCAGGGATGGGGAGGAGCTGGCATGGTGCTG
GGGAAGCGGCAATGCCAGACTGGGACTTGAAGAAGCACCTGCAGAGACCAGAGAAACCAAAAAGTGGTGCTGCGAATAAC
CAGTTGCCAACCTCCCAGCCAAGCCTCAGGCACAAGGTGGATGAGCACGAACAAGATGGCAACGAGCTACAGACCACCCT
TGAGTTCCAAGCCCACGTAGCCAAGAAGCTAGGAGCCCTACTGGACAGCTTCATTACCGTCTCGAAGTAGCAAAGGAGCC
AGCAAAAGCTGAAGTTCAGAAAATCGCCTCAGAGGATGATGGCTTACACCTTTTCTTCACGTCCATTCCTGGAGTCCCTG
AGAAGGAAGCTTCTCCCCAACCCTGCTGCAGGCGACAGCCTTTTACCTCCAGCAGCAGCGAGGACAGTGACGAGGAGTGG
CAGCGGTGCTGGGAGGCAGCTGTGTCAGTATCCGACATCCTCCAGGAGTCAGCCATCCACAGCCCTGTCAGGAAGGAGAA
GGAGACAAGAAAGAAAAGGAAGTGGAAAAAGGAAGCCAAGAAGGTGGCCAGTGTCGACTTGGCTATAACCACCACTATCA
CCACCAATGGAGCTATGGTCCAGAAGCAGGAGAAGGAATCAGGCAAGCCCAACGGGGACCGGCTGCTGCTTGGGACCAAA
AAGGAAAAAAAGAAAGAAAAAGGCCAAGAAGGCCAGCAAATCTTCTCTGTTTCCACCAGCAAAGAGTGCTACAGCTATGC
CTGCAAAC

Alignment

ORF - retro_tsyr_257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAVFSGAVRDSENGSSGSDGEELA-RSQEVAIPSWDLKKGLQGPEKPRSGAANNQLRASQPSLRHKVDEH
          M....GA..DSE..S...DGEELA....E.A.P.WDLKK.LQ.PEKP.SGAANNQL..SQPSLRHKVDEH
Retrocopy MVALNGATSDSESSSGSRDGEELA>GAGEAAMPDWDLKKHLQRPEKPKSGAANNQLPTSQPSLRHKVDEH

Parental  EQDANELQTTLEFR-HVAK-LGALLDSFITIS-EVAKEPAKTEVQKVASEDDGFRLFFTSIPGGPEKEAS
          EQD.NELQTTLEF..HVAK.LGALLDSFIT.S.EVAKEPAK.EVQK.ASEDDG..LFFTSIPG.PEKEAS
Retrocopy EQDGNELQTTLEFQAHVAKKLGALLDSFITVS<EVAKEPAKAEVQKIASEDDGLHLFFTSIPGVPEKEAS

Parental  P-PCHRRQPSTSSS-EHSDEEWQRCWEAAVSVSDILWESAIHSPVREEKEARKKRKSEKKAKKAASVHSA
          P.PC.RRQP.TSSS.E.SDEEWQRCWEAAVSVSDIL.ESAIHSPVR.EKE.RKKRK..K.AKK.ASV..A
Retrocopy PQPCCRRQPFTSSSSEDSDEEWQRCWEAAVSVSDILQESAIHSPVRKEKETRKKRKWKKEAKKVASVDLA

Parental  VTTTVTTNGAMVQKQE-ESGKPNGDQMLFGTKKKKRKEKAKKASE-ASLFPPAKSAAAVPAN
          .TTT.TTNGAMVQKQE.ESGKPNGD..L.GT................SLFPPAKSA.A.PAN
Retrocopy ITTTITTNGAMVQKQEKESGKPNGDRLLLGTXXXXXXXXGQEGQQ>SSLFPPAKSATAMPAN

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_257 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
Dasypus novemcinctus	ENSDNOG00000000382	1 retrocopy	retro_dnov_1611,
Microcebus murinus	ENSMICG00000008728	2 retrocopies	retro_mmur_628, retro_mmur_84,
Tarsius syrichta	ENSTSYG00000009317	2 retrocopies	retro_tsyr_2056, retro_tsyr_257 ,