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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagagatgggttggtttgtttatgccatcaaatactgcaaacaaattttggtttgatacctgtttcctgttaacttcatgtagctacgtttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAAATATGGGAAGAGCTTTCTAAAGCAAAATACATGGAGTGGGAACTGGTTT

Basic information

species Arabidopsis thaliana
transcript AT3G07370.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G07370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G104769_T02 (Zea mays), 3'ss of exon 4
--actagagatgggttggtttgtttatgccatcaaatactgcaaacaaattttggtttgatacctgtttcctgttaacttcatgtagctacgtttcata----tagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAAATATGGGAAGAGCTTTCTAAAGCAAAATACATGGAGTGGGAACTGGTTT
  | | | ||    ||   ||||||  || |  || |  |  || | |||||   | |  |  |  |||  || | | |  |   | ||   |||   |    ||| | || || ||||||||  |  |  ||||  || | || ||||| ||||| |||||| | ||||||||||||||||||||||| || |||||     | |
ctatttg-gacaaattatgttgtttgagctagaaatt--tagaatctaatttctctctatt--ccattttttgatga-tgaacaaaactttttttttcaaaactagTCCTTGGAGCTTGGAAGGGGTGCACATCCTGCAAGCTACATGGTTGAAGAGATATGGCAGGAGCTTTCTAAAGCAAAATACATCGAATGGGAGAGCTTAT

upper sequence: AT3G07370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G09930.2 (Glycine max), 3'ss of exon 2
actagagatgggttggtttgtttatgccatcaaatactgcaaacaaatttt----ggtttgatacctgtttcctgttaact-tcatgtagctacgtttcatat--agGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAAATATGGGAAGAGCTTTCTAAAGCAAAATACATGGAGTGGGAACTGGTTT
      ||||   |  | ||   ||   | ||   | |  |  |   ||||      ||| ||  |   |  ||| | | | || | | | |     |||||   ||||||| |||||||||||| |  | ||||| |  || ||||||||||||||||||||| |||||||| | || ||||||||| | |||||||| |     |
------gatgatcttttctgag-atattaacagtgattttatcctttttttttttaatttcatttcaaatgtctgatgattctcctattgtttgtgatcataataagGCTTTGGATCTTGGAAGAGGTGCCAATCCCAAGGGCTATATGGTAGAAGAAATATGGCAAGAGCTTGCAAAGGCAAAATACCTTGAGTGGGAGCGATCAT

upper sequence: AT3G07370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G22210.2 (Glycine max), 3'ss of exon 4
actagagatgggttggtttgtttatgccatcaaatactgcaaacaaattttggtttgatacctgtttcctgttaact-tcatgtagctacgtttcatat---agGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAAATATGGGAAGAGCTTTCTAAAGCAAAATACATGGAGTGGGAACTGGTTT
  |   |||| | |  | ||   ||   | ||  || |   | |   ||||  ||| ||  |   |  ||| | | | || | | ||| |   |||||    ||||||| |||||||| ||| |  | ||||| |  || ||||||||||||||||||||| |||||||| | || ||||||||| | ||||||||||   | |
--tgatgatgcgcttttctgag-atattaacagttatt-tgatccttttttaatttcatttcaaatgtctgatgattctcttattgcttctgatcataattaagGCTTTGGATCTTGGGAGAGGTGCCAATCCCAAGGGCTATATGGTAGAAGAAATATGGCAAGAGCTTGCAAAGGCAAAATACCTTGAGTGGGAACGATTAT

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|86048653|gb|DR344408.1|DR344408
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTT
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTT
EST: gi|86048650|gb|DR344405.1|DR344405
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGARTTGCAAAGG                         GCTTTAGATCTTG
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTG
EST: gi|86048663|gb|DR344418.1|DR344418
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATAT
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATAT
EST: gi|86048652|gb|DR344407.1|DR344407
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACATGATATATGGTAGAAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
EST: gi|86048659|gb|DR344414.1|DR344414
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
EST: gi|86048665|gb|DR344420.1|DR344420
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTSGAAGATGCTCGAATCCAACAGGATATATGGTAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAA
EST: gi|86048657|gb|DR344412.1|DR344412
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
EST: gi|86048661|gb|DR344416.1|DR344416
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
EST: gi|86048658|gb|DR344413.1|DR344413
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACATGATATATGGTAGAAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
EST: gi|86048660|gb|DR344415.1|DR344415
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACATGATATATGGTAGAAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
EST: gi|86048664|gb|DR344419.1|DR344419
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGA-GAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
EST: gi|86048654|gb|DR344409.1|DR344409
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAG
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAG
EST: gi|86048656|gb|DR344411.1|DR344411
EST:     CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGG                         GCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA
genomic: CATTATTGCAGAAGAAAGAATTTACTAATGGAGTCAAAGAATTGCAAAGGgtaaggatct ... tttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttggtttgatacctgtttcctgttaacttcatgtagctacgtttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAAATATGGGAAGAGCTTTCTAAAGCAAAATACATGGAGTGGGAACTGGTTT
                        tgttaac  putative branch site (score: 2)
                                             tttcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagagatgggttggtttgtttatgccatcaaatactgcaaacaaattttggtttgatacctgtttcctgttaacttcatgtagctacgtttcatatagGCTTTAGATCTTGGAAGATGCTCGAATCCAACAGGATATATGGTAGAAGAAATATGGGAAGAGCTTTCTAAAGCAAAATACATGGAGTGGGAACTGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - ggtttgt
- - - - - - - - - - - - - - - caaatac
- - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ggtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacttca