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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaggtatgttttgcctttatggaagttcaaatttttgttgtttaggttttcctgatgcattattggaccttatatattaacagatttgtttttgtagACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAACAGTTGCTTGCTGCTGAGGTAGAAGCTCAACACATTGTCAATGCTGCAA

Basic information

species Arabidopsis thaliana
transcript AT3G01390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G33790.1 (Glycine max), 3'ss of exon 1
ttttaggtatgttttgcctttatggaagttcaaatttttgttgtttaggttttcctgatgcattattggaccttatatattaacagatttgtttttgtagACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAACAGTTGCTTGCTGCTGAGGTAGAAGCTCAACACATTGTCAATGCTGCAA------
    ||   |  ||||  ||  |  | |  |  |||| ||||   ||  |||   | |    | |||  |||  |  | |||| ||     || |     | |||| |     | || |||| ||||||||| |||||||||   || ||||||||||| ||||||||   |||||| |||   ||||||||||||||||      
---aagaacttgtttgtgttgcttaaggacctgatttatgtt---tacttttctattaattttgatttaacc--acttgttaatag-----ttatcaaccaattttat----cacagAATGGCATCCAACAGGGGTCAAGGTGGAATTCAACAGTTGCTGGCTGCTGAACAAGAAGCGCAAAGAATTGTCAATGCTGCAAAAAATG
















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|164191557|gb|ES127262.1|ES127262
EST:     GAATCAACAAAG                         ACTTTTGTGCAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAA
genomic: GAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAA
EST: gi|125197975|gb|EL212929.1|EL212929
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCATGG
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGG
EST: gi|125322674|gb|EL336759.1|EL336759
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCA
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCA
EST: gi|164026946|gb|ES111442.1|ES111442
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGCAATAAAGC
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGC
EST: gi|125256957|gb|EL271042.1|EL271042
EST:     ATAGTATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCA
genomic: ATAG-ATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCA
EST: gi|125079830|gb|EL141665.1|EL141665
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCATGGAA
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGGAA
EST: gi|125032746|gb|EL105015.1|EL105015
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCA
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCA
EST: gi|125036864|gb|EL109133.1|EL109133
EST:     ATAGATCCTCGATTTTCTCTCTTCTCTCTTAGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATA
genomic: ATAGATCCTCGATTTTCTCTCTTCTCTCTT-GTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATA
EST: gi|124764677|gb|EH854807.1|EH854807
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCATGGAA
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGGAA
EST: gi|125239787|gb|EL253872.1|EL253872
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCATGGAA
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGGAA
EST: gi|125186144|gb|EL201098.1|EL201098
EST:     CCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAA
genomic: CCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAA
EST: gi|164045289|gb|ES196690.1|ES196690
EST:     CTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGCAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAA
genomic: CTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAA
EST: gi|125322458|gb|EL336543.1|EL336543
EST:     GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCA
genomic: GATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCA
EST: gi|124995918|gb|EL068187.1|EL068187
EST:     ATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAG                         ACTTTTGTGTAATAAAGCATGGAAT
genomic: ATAGATCCTCGATTTTCTCTCTTCTCTCTTGTCCTCGGAATCAACAAAGgtaatgtgtc ... gtttttgtagACTTTTGTGTAATAAAGCATGGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggttttcctgatgcattattggaccttatatattaacagatttgtttttgtagACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAACAGTTGCTTGCTGCTGAGGTAGAAGCTCAACACATTGTCAATGCTGCAA
                                tattaac  putative branch site (score: 1)
                                          tttgttttt  putative PPT
                           ttatatattaacagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaggtatgttttgcctttatggaagttcaaatttttgttgtttaggttttcctgatgcattattggaccttatatattaacagatttgtttttgtagACTTTTGTGTAATAAAGCATGGAATCCAACAGAGGTCAAGGTTCGATCCAACAGTTGCTTGCTGCTGAGGTAGAAGCTCAACACATTGTCAATGCTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - -tgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacagat