RetrogeneDB ID: retro_tsyr_202

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_5176:72207..72789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSL1
• Ensembl ID: ENSTSYG00000003900
• Aliases: None
• Description: NSL1, MIS12 kinetochore complex component [Source:HGNC Symbol;Acc:24548]

Sequence

>retro_tsyr_202
ATGGCGGAGGCTTCTGAGTTGGTGGTCCTCCACTCTCCCGCGAGCAAGGACATGACGGCGGAGACAAACAGCCAGGCCTT
GGAACCCAACACTCTACAAGAGGAATTTCGGGTGCGCAGCACTTCGAAGCGGACTGTGACGGAAATGCTACAGCTGTGCA
GTTGCTTCGTGCAAAAGCTCAGGGACACTCTCCTGGAGGAGATTCAGGAGCCCGCCCTGCAAGACGCGCAGTGGATTTTT
GAGTCAGCTGTGCAAGAGAATGTCAGCATTAATGGGCAAGCATGGCAGGACACTTTAGATGATTGTCTTATGGATTCTGA
CATCAAAGAACTTGAAGATCAGTTTGACGAAATCATAGTAGATATAGCAACAAAACATAAGCAGTATCCCAGAAAGATCC
TGGAATGTGTCATCAAAATCATAAAAGCAAAATAAGAAATTCTGAAGCAGTACCACCCTGTTGTATATTCATTGGTCCTA
AAATGTGACCCTGATCTAGACTCTCATATGGAAAATTTGAAATGCAGAGGAGAAACAATAGCTAAGGAGATCAGTGAAAC
CACGAAGTCCTTGCCTACACTA

Alignment

ORF - retro_tsyr_202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.02 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGVSELVVLQPLGSKDIMAETDSQALVPHTLQEDFRVRCTSKRAVTEMLQLCSCFVQKLGDALPEEIRE
          MA..SELVVL....SKD..AET.SQAL.P.TLQE.FRVR.TSKR.VTEMLQLCSCFVQKL.D.L.EEI.E
Retrocopy MAEASELVVLHSPASKDMTAETNSQALEPNTLQEEFRVRSTSKRTVTEMLQLCSCFVQKLRDTLLEEIQE

Parental  PALRDAQWIFESAVQENVSINGQAWQDTSDDCLMDSDIKELEDQFDEIIVDIATKRKQYPRKILECVIKI
          PAL.DAQWIFESAVQENVSINGQAWQDT.DDCLMDSDIKELEDQFDEIIVDIATK.KQYPRKILECVIKI
Retrocopy PALQDAQWIFESAVQENVSINGQAWQDTLDDCLMDSDIKELEDQFDEIIVDIATKHKQYPRKILECVIKI

Parental  IKAKQEILKQYHPVVHPLDLKCDPDPGSHMENLKCRGETIAREISEAMKALPTL
          IKAK.EILKQYHPVV..L.LKCDPD..SHMENLKCRGETIA.EISE..K.LPTL
Retrocopy IKAK*EILKQYHPVVYSLVLKCDPDLDSHMENLKCRGETIAKEISETTKSLPTL

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_202 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001862	1 retrocopy	retro_chof_464,
Rattus norvegicus	ENSRNOG00000042286	1 retrocopy	retro_rnor_2027,
Tarsius syrichta	ENSTSYG00000003900	1 retrocopy	retro_tsyr_202 ,
Tursiops truncatus	ENSTTRG00000016584	1 retrocopy	retro_ttru_564,