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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaatcattaattgaatctatcgatttggattataatcatatctgtgtttttggattcggattttgatctaatggttatgaatttgggatcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACAGTTGCGGATATGATCAAAGGAAAGACTCCAGAAGAGATCCGCACAACGT

Basic information

species Arabidopsis thaliana
transcript AT1G75950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08440.1 (Glycine max), 3'ss of exon 1
accaatcattaattgaatctatcgatttggattata-atcatatctgtgtttttgg-attcggattttgatctaatggttatgaatttggga---tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACAGTTGCGGATATGATCAAAGGAAAGACTCCAGAAGAGATCCGCACAACGT
        ||  |    | | |  |||   ||   | || |  ||||| | ||| | |     | | ||  |||||   ||| ||| ||  |   |  | |  |||||||||| ||| |||| ||||||| | |||| || || |||||||| || || || || |||||||| || ||||||||||| || || ||||  || |
-----atgtttgtattgtttgtgcattgcaatgccacataaactctgtttatttagtaggttaagtctgtactaatacatattaatgtgacaattttctttttagGCTGCTAACTACTTGAACATCAAGAGCCTGCTGGACCTTACATGTCAAACTGTAGCCGACATGATCAAGGGGAAGACTCCAGAGGAAATTCGCAAGACCT
















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|125250327|gb|EL264412.1|EL264412
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTG
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTG
EST: gi|164126502|gb|ES025353.1|ES025353
EST:     CGGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACC
genomic: C-GCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACC
EST: gi|47831175|gb|CK120859.1|CK120859
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|86062163|gb|DR357920.1|DR357920
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|164125851|gb|EL976900.1|EL976900
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTAC
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTAC
EST: gi|124822122|gb|EH906988.1|EH906988
EST:     TCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: TCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|124940730|gb|EL017155.1|EL017155
EST:     CGCTGATTTTATTGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATA
genomic: CGCTGATTTTA-TGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATA
EST: gi|124972578|gb|EL046263.1|EL046263
EST:     CTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGGTCTAACATGTCAGACA
genomic: CTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|124927392|gb|EL005133.1|EL005133
EST:     CTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: CTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|86087187|gb|DR382946.1|DR382946
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATYTAACATGTCAGACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|125012916|gb|EL085185.1|EL085185
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATA
EST: gi|47830811|gb|CK120495.1|CK120495
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|124751953|gb|EH842083.1|EH842083
EST:     CTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: CTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|124949954|gb|EL025458.1|EL025458
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAAATATCAAGAACTTGCTTGATCTAACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAA-TATCAAGAACTTGCTTGATCTAACA
EST: gi|86062118|gb|DR357875.1|DR357875
EST:     AC-CTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|86062126|gb|DR357883.1|DR357883
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|116482973|gb|EG525565.1|EG525565
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|164018110|gb|ES211919.1|ES211919
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGA
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGA
EST: gi|164202902|gb|ES081193.1|ES081193
EST:     AACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: AACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|164120716|gb|ES037510.1|ES037510
EST:     CTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
genomic: CTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACA
EST: gi|124793988|gb|EH883667.1|EH883667
EST:     ATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAG
genomic: ATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAG
EST: gi|163984144|gb|ES174542.1|ES174542
EST:     ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTG                         GCTGCTAATTACCTGAATATC
genomic: ACGCTGATTTTATGAAGATCGATCAAGCTACTCTCTTTGAACTCATTCTGgtatgtttct ... tcttgtgcagGCTGCTAATTACCTGAATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttttggattcggattttgatctaatggttatgaatttgggatcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACAGTTGCGGATATGATCAAAGGAAAGACTCCAGAAGAGATCCGCACAACGT
                      atctaat  putative branch site (score: 3)
                               ttatgaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accaatcattaattgaatctatcgatttggattataatcatatctgtgtttttggattcggattttgatctaatggttatgaatttgggatcttgtgcagGCTGCTAATTACCTGAATATCAAGAACTTGCTTGATCTAACATGTCAGACAGTTGCGGATATGATCAAAGGAAAGACTCCAGAAGAGATCCGCACAACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
-ccaatca
- - - - - - - - - - - -gatttgg
- - - - - - - - - - - - - - - - - -aatcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatttgg