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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttacccggctttcggtacacataactctctctgttgtaattattatcatcgtaatattttattcaatattcatggtcctgcttctttttcagag...

Basic information

species Arabidopsis thaliana
transcript AT2G20360.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20360.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os02g57180.2 (Oryza sativa), 5'ss of exon 5
TATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttacccggctttcggtacacataactctctctgttgtaattattatcatcgtaatattttattcaatattcatggtcctgcttctttt--tcagag----------------------
||| || ||||||| ||||||||| || |  || |||||||| |||||||||||||| || |||||||  |||||| |||| ||||| | | | ||||||||    | | |    ||  |  | ||  |||||    |  |  | |    |   |   ||      ||     ||| ||| |     ||  |||   || |                       
TATCCAGGTTTCTTCCCTAGGAGCATCGGCCTCTTCTCCTTCTAGAATGCTGAGGGCCAAGGCTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAGgtga--tcatctacattaggcaatactgaactcctgtttctacattaccgaaagttagaagcaaacatgtcccatttatgttggcagttactttaaccaaaattttgtttgcatggatcaacag

upper sequence: AT2G20360.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv07s0005g04440.t01 (Vitis vinifera), 5'ss of exon 7
TATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttacccggctttcggtacacataactctctctgttgtaattattatcatcgtaatatttt-attcaatattcatggtcctgcttctttttcagag-
|||||||||||||||| |||| || |||   |||||||| || || ||| | | ||| ||||||||||| ||||||||||| ||||  | | | ||||||||  |  ||      ||| | |  |      |||   || |||   || |  ||  | |   |    |  |      |                        
TATTCAAGTTTCTTGCTTAGGGGCATCTCCATCATCTCCATCTAGGATGTTAATGGCTAAAGCTGCTGCAGAGGAAGCTGTTTTGAGAGAATTACCTGAGgtgaaactatt--atttttgctcgagtctgatctgattgatgtggctacttccaatggatcttccccaccccccccccccnnnnnnnnnnnnnnnnnnnnnn
















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|116387772|gb|EG430364.1|EG430364
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116401381|gb|EG443973.1|EG443973
EST:     TGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377195|gb|EG419787.1|EG419787
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|124855581|gb|EH940018.1|EH940018
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAA
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAA
EST: gi|116401379|gb|EG443971.1|EG443971
EST:     GGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377193|gb|EG419785.1|EG419785
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|164214029|gb|ES099135.1|ES099135
EST:     CTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: CTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116401374|gb|EG443966.1|EG443966
EST:     GGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|163993592|gb|ES082836.1|ES082836
EST:     GGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116401371|gb|EG443963.1|EG443963
EST:     GAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|86048714|gb|DR344469.1|DR344469
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116401376|gb|EG443968.1|EG443968
EST:     GAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116383740|gb|EG426332.1|EG426332
EST:     GGGCAAAAGCCGTTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377192|gb|EG419784.1|EG419784
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377191|gb|EG419783.1|EG419783
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116383739|gb|EG426331.1|EG426331
EST:     GGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377190|gb|EG419782.1|EG419782
EST:     CGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116383744|gb|EG426336.1|EG426336
EST:     GGGCAAAAGCTCGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: GGGCAAAAGCT-GCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377199|gb|EG419791.1|EG419791
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAAACATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116387790|gb|EG430382.1|EG430382
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377200|gb|EG419792.1|EG419792
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|47828656|gb|CK118340.1|CK118340
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|164156982|gb|ES090230.1|ES090230
EST:     AAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTAC
genomic: AAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTAC
EST: gi|116377196|gb|EG419788.1|EG419788
EST:     TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
EST: gi|116377187|gb|EG419779.1|EG419779
EST:     CGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAG                         GCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG
genomic: TGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttac ... tgttttgtagGCAACCATCATGAGACCTGCAACCATGATTGGTACAGAAGACAGAATCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTGCTGAGGAAGCTGTCTTGAACGCACTGCCTGAGgtatacttacccggctttcggtacacataactctctctgttgtaattattatcatcgtaatattttattcaatattcatggtcctgcttctttttcagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctttttc