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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttctgttacaactcatgtaggactaaccttttgcttttctcattgtatggacattatcctgttagaaatcaatctcctatccgaacatccactagtgcaataacatatgtgtagaaaagtacctttcaaatttttacttagtatttggcttaataaatatgaaaagtttttttgttatgtatttcagGACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGATGATCATTGGCTTTGGGATCCTGACTTCACAATTGCGTCCAA

Basic information

species Arabidopsis thaliana
transcript AT5G12200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 6
gttttctgttacaactcatgtaggactaaccttttgcttttctcattgtatggacattatcctgttagaaatcaatctcctatccgaacatccactagtgcaataacatatgtgtagaaaagtacctttcaaatttttacttagtatttggcttaataaatatgaaaagtttttttgttatgtatttcagGACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGATGATCATTGGCTTTGGGATCCTGACTTCACAATTGCGTCCAA
                                                                            ||   | | | | |     |      |||    || |   |||  |   |  |  | |   |  ||||||  |||  ||    |||           |||   |    || |||| ||||  || || || || ||||| || |||||| || | |||||||||  |||||||||||||||||||||||| ||||| || ||
----------------------------------------------------------------------------ctgagaactggatactttttga---gatagatcatttactgaat-gcctcgcttgactcaatttttagtaactggactaggttatac----------tttaaaaaactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA

upper sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
gttttctgttacaactcatgtaggactaaccttttgcttttctcattgtatggacattatcctgttagaaatcaatctcctatccgaacatccactagtgcaataacatatgtgtagaaaagtacctttcaaatttttacttagtatttggcttaataaatatgaaaagtttttttgttatgtatttcagGACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGATGATCATTGGCTTTGGGATCCTGACTTCACAATTGCGTCCAA
                                                                     |    || ||  | | |||| ||   |  |||||  |    | | |     | |   ||| |   | ||| | || |          |||  ||  |      |||| || || | | ||||||||| ||||||||||||||| || || ||||| ||| |||||||||||  | |||| ||||||||||||||||  |  ||  | ||
--------------------------------------------------------------------taggtgatatctgaactgaacttc---tgatgcaactat---tatctgatctaatgattttgag--tcttaatcagga---------gtaaccattca-----cttttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125089233|gb|EL147678.1|EL147678
EST:     GACGAGATTCGCTAAAGCTCGAAAATCAG                         GACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGA
genomic: GACGAGATT-GCTAAAGCTCGAAAATCAGgttttctgtt ... tgtatttcagGACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacttagtatttggcttaataaatatgaaaagtttttttgttatgtatttcagGACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGATGATCATTGGCTTTGGGATCCTGACTTCACAATTGCGTCCAA
               gcttaat  putative branch site (score: 4)
                 ttaataaatatgaaaa  TA-rich tract