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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcacataactgtactgttttaggatatctttagattggatcatgttttagttagaagaatggatcataagctaatgaatgtgtgtttgatgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGAAAGAAGCAACTTAGCAAACTCAGAGCTAAGGCCGAGAAGGTTGCTGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G07110.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G07110.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 3
atcacataactgtactgttttaggatatctttagattggatcatgttttagttagaagaatggat-cataagctaatg--aatgtgtgtttgatgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGAAAGAAGCAACTTAGCAAACTCAGAGCTAAGGCCGAGAAGGTTGCTGAAG---
     | || | |    ||||    | | ||| | ||    ||  |   |     |  ||| |||   |  ||| |||  | |   ||||| ||    |  | |||||||| || || |||||||||||||  || |||   |||||||||||||||||||| || | |||| | || |  || |||||||||||||||||||   
---ggaaaattttggatttttttttttttttttgcttt--ccaaatggaaagggaataaatagatgtgtttgctgatgtgagtaattgttttattgctaaca-cagGAGCTAGAAAAGAAGAGAAAGGAAAAGGCACAATTGGTTTATGAGAGAAAGAAGCAGCTCAACAAATTAAGGGTGAAAGCCGAGAAGGTTGCTGAAGACA
















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|47832259|gb|CK121943.1|CK121943
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|116476045|gb|EG518637.1|EG518637
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|116476043|gb|EG518635.1|EG518635
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|47828023|gb|CK117707.1|CK117707
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|116476053|gb|EG518645.1|EG518645
EST:     TGGGTCGCCTTTTTTCTGAAGTCGGGGGGAACCACTACGACCCCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|116476052|gb|EG518644.1|EG518644
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|86071402|gb|DR367159.1|DR367159
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAA
EST: gi|47828463|gb|CK118147.1|CK118147
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|86071400|gb|DR367157.1|DR367157
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACC--CAT-                         CAGGAGCTGGAGAACA-GAGAAAGGAAA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAA
EST: gi|86071403|gb|DR367160.1|DR367160
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|47830930|gb|CK120614.1|CK120614
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|116476054|gb|EG518646.1|EG518646
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAG                         --G-AGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
EST: gi|116476044|gb|EG518636.1|EG518636
EST:     TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATC-A-                         -AGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA
genomic: TGGGTCGCCTTTCTTCTGAAGTCGGGTGGAACCACTACGACACCATCAAGgtatgcttca ... tgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagttagaagaatggatcataagctaatgaatgtgtgtttgatgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGAAAGAAGCAACTTAGCAAACTCAGAGCTAAGGCCGAGAAGGTTGCTGAAG
                           taatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcacataactgtactgttttaggatatctttagattggatcatgttttagttagaagaatggatcataagctaatgaatgtgtgtttgatgaaaatgagCAGGAGCTGGAGAACAAGAGAAAGGAAAGAGCTCAAGCTGTTTATGAGAGAAAGAAGCAACTTAGCAAACTCAGAGCTAAGGCCGAGAAGGTTGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- cacataa
- - - - - - - - gttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttga