RetrogeneDB ID: retro_tsyr_2108

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_91786:6384..7206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD20
• Ensembl ID: ENSTSYG00000012406
• Aliases: None
• Description: potassium channel tetramerization domain containing 20 [Source:HGNC Symbol;Acc:21052]

Sequence

>retro_tsyr_2108
CCATCCATTTTTACTGCACAGCCAAATACAATGTTGGGCAGGATGTTTGGATCTGGCAGAGAACACAACTTTACACGTCC
CAATGAGAAGGGAGAATAGGAGGTGGCAGAGGGAATTGGTTCCACTGTGTTTCGAGCTACTCTGGATTACTACAAAACGG
GAATAATTCGTTGTCCTGATGGCACATCAATTCCTGAACTGAGAGAAGCATGTGACTATCTTTGTATCTTTTTCGAATAT
AGTACTATTAAATGTAGAGATCTCAGTGCCCTTATGCATGAGTTATCAAATGATGGTGCTCGTAGACAATTTGAATTTTA
TCTGGAAGAAATGATCCTTCCTCTCATGGTAGCTAGTGCCCAGAGTGGAGAACGAGAATGCCATATAGTGGTGCTTACAG
ATGATGATGTGGTTGATTGGGATGAAGAGTATCCATCACAGATGGGAGAAGAATATTCACAGATTATTTATAGCACAAAA
TCATATAGATTTTTCAAGTACATTGAAAACAGAGATGTGGTCAAATCAGTTTTGAAGGAGAGGGGTCGTAAGAAGATTAG
ATTGGGAATAGAAGGTTATCCTACCGACAAAGAAAAAGTAAAGAAGAGGCCTGGGGGCCACCCAGAAGTGATTTACAACT
ATGTCCAAAGACCATTTATTCGAATGTCCTGGGAGAAGGAAGAAGGAAAGAGTCGGCATGTAGACTTTCAGTGTGTAAAG
AGTAAATCCATCACTAACCTCGCAGCAGCTGTGGCAGACATTCCCCAGGACCAGCTGGTGGTCATGCACCCAACTCCGCA
AGTGGATGAGGTGGATATTCTC

Alignment

ORF - retro_tsyr_2108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.26 %
• Parental protein coverage: 64.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQIFTAHPDTMLGRMFGPGREYNFTRPNEKGEYEIAEGISATVFRSVLDYYKTGIINCPDGISIPDLRDT
          P.IFTA.P.TMLGRMFG.GRE.NFTRPNEKGE.E.AEGI..TVFR..LDYYKTGII.CPDG.SIP.LR..
Retrocopy PSIFTAQPNTMLGRMFGSGREHNFTRPNEKGE*EVAEGIGSTVFRATLDYYKTGIIRCPDGTSIPELREA

Parental  CDYLCINFDFNTIRC----ALLHELSNDGAHKQFDHYLEELILPIMVGCAKKGERECHIVVLTDEAPMWW
          CDYLCI.F...TI.C....AL.HELSNDGA..QF..YLEE.ILP.MV..A..GERECHIVVLTD.....W
Retrocopy CDYLCIFFEYSTIKCRDLSALMHELSNDGARRQFEFYLEEMILPLMVASAQSGERECHIVVLTDDDVVDW

Parental  NS--PPPMGEEYSQILYSSKLYRFFKYIENRDVAKTVLKERGLKNIRIGIEGYPTCKEKIKRRPGGRSEV
          ....P..MGEEYSQI.YS.K.YRFFKYIENRDV.K.VLKERG.K.IR.GIEGYPT.KEK.K.RPGG..EV
Retrocopy DEEYPSQMGEEYSQIIYSTKSYRFFKYIENRDVVKSVLKERGRKKIRLGIEGYPTDKEKVKKRPGGHPEV

Parental  IYNYVQRPFIQMSWEKEEGKSRHVDFQCVRSKSLTNLVAAGEDVLEDQEILMHHPPQVDELDRL
          IYNYVQRPFI.MSWEKEEGKSRHVDFQCV.SKS.TNL.AA..D...DQ...MH..PQVDE.D.L
Retrocopy IYNYVQRPFIRMSWEKEEGKSRHVDFQCVKSKSITNLAAAVADIPQDQLVVMHPTPQVDEVDIL

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_2108 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017166	1 retrocopy	retro_ecab_55,
Myotis lucifugus	ENSMLUG00000007139	1 retrocopy	retro_mluc_1744,
Tarsius syrichta	ENSTSYG00000000445	2 retrocopies	retro_tsyr_196, retro_tsyr_367,
Tarsius syrichta	ENSTSYG00000012406	1 retrocopy	retro_tsyr_2108 ,