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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctcttctcattctaaatttgcatattgttcatacaaatcggacatttgatctgattgtttctcataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 10
-------gtatatctcttctcattctaaatttgc--atattgttcatacaaatcggacatttgatctgattg---------tttctcataaattagGTT--CTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC------------
          |||  ||    |||  | |  |||    ||||  |||    ||  | | ||| |  ||| ||           | || | | | |   |  |||||| | | | |  | |    |     | |   ||  ||| | | ||||   |  |   |     |     |  ||    ||  | |  |  ||             
gtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcagTACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAACGAGATGGCTGAGGTCCTTATGGACTTCCCACAATTGACAATGACATTGC

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
gtatatctcttctcattctaaatttgcatattgttcatacaaatcggacatttgatctgattgtttc--tcataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC
     | |  | || ||  |  |    |||||||   | | |||   | | ||| ||  | |  |||  | ||   | ||||||| |||||||| || ||| | |||||||| || |||||||| ||||| |||||||||||||| ||||| ||||| || |||||||| || |||||||
----gtatgctttcctttcatttgcaaatattgtgttt-ctaattttagagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 11
gtatatctcttctcattctaaatttgc---atattgttcatacaaatcggacatttgatctgattgtttc--tcataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC
| || | |  | |     ||  | |     |||||||   |   | |   ||| ||| ||  | |  |||  | ||   | ||||||| |||||||| || ||| | |||||||| || |||||||| ||||| |||||||||||||| || || ||||| || |||||||| || |||||||
gcatgttttattttcagttacttctatcaaatattgtgtttcttagttt-acagttggtcaaactaattcaatgattgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGCACAACACTAGTGGCTAACACTTCAAACATGC

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 11
gtatatctcttctcattctaaatttgcatattgttcatacaaatcggacatttgatctgattgtttctcataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC
                                           | ||   ||  |||| |   |     | || ||||||||| ||||| || || ||| ||||||||||  ||||||||||  | || ||||||||||||||  | || || || || |||||||| ||||||||||
-----------------------------------------gtttgg---ttcaatctaaa-atacaataaaatttagGTTCTGATGGATTTTCCTCAACTGACAATGACACTGCCTGATGGGAGAGAAGAATCTGTCATGAAGAGAACTACGCTCGTAGCTAACACTTCTAACATGC

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
----gtatatctcttctcattctaaatttgcatatt--gttcatacaaatcggacatttgatctgattgtttctca-taaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC
    ||   | ||||||| ||  ||   |    | |  |||   |||  | ||| ||||    |    ||| || | | | | ||||||||||||| || || |||||||| |||||  |||||||||||||||| |||||||||||||| || || |||||||| || ||||| || || ||||
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC

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|116463760|gb|EG506352.1|EG506352
EST:     ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCGTGATGGCCGTGAG
genomic: ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
EST: gi|164211749|gb|ES085155.1|ES085155
EST:     ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
genomic: ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
EST: gi|116482299|gb|EG524891.1|EG524891
EST:     ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATG
genomic: ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATG
EST: gi|124960584|gb|EL035242.1|EL035242
EST:     TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAAATGACGTTGCCTGATGGCCGTGA
genomic: TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAA-TGACGTTGCCTGATGGCCGTGA
EST: gi|124754717|gb|EH844847.1|EH844847
EST:     GTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAA
genomic: GTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAA
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
genomic: ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
EST: gi|125100559|gb|EL155962.1|EL155962
EST:     TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
genomic: TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatattgttcatacaaatcggacatttgatctgattgtttctcataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC
                               atctgat  putative branch site (score: 4)
                                     ttgtttctc  CT-rich tract
                                        tttctcataaatta  TA-rich tract