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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcctattatttgtgtgttacataagttgttgcatatagattctgttttttatttacgtgattgtttgtcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG

Basic information

species Arabidopsis thaliana
transcript AT2G44120.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 2
gtatgtgcctatt--atttgtgt-gttacataagttgttgcatatagat-----tctg-ttttttatttacgtgattgtt-------tgtcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG
||| |   | | |  | |||| | |||| | | ||   ||  |||||||     |||| || | | || | |  | ||||       |||    || ||||||||||||||  |||| || |||| ||||||| |||||||| |||||||||| |||
gtaaggaaccacttaagttgtattgttata-atgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 3
gtatgtgccta--ttatttgtgtgttaca----taagttgttgcatatagattctgttttttatttacgtgattgtt---tgtcatttg--------cagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG
|||  |   ||  |||||  ||| | | |    || | |  |  ||     || || || || ||    | |||| |   ||  ||||         ||||||||||||||| || || ||||| | ||||||||||||||| |||||||||||||||
gtaattaattaatttattaatgtatcataacattatgctagtatattgtctttttggttattgttgtttttattgctaaatggaatttatgtaatgtcagTATCAATGCCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
--------------------gtatgtgcctattatttgtgtgttacataagttgttgcatatagattctgttttttatttacgtgattgtt--------tgtcatttg--------cagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG
                     ||  |   || |||||   | |  ||| |  |  |     || ||| | |||||  ||   ||  || ||        || | |||         ||||||||||||||| || || ||||| | ||||||||||||||| |||||||||||||||
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG

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|164081405|gb|ES167220.1|ES167220
EST:     GGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: GGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036885|gb|DR332640.1|DR332640
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036872|gb|DR332627.1|DR332627
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|164121522|gb|ES012486.1|ES012486
EST:     TGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036886|gb|DR332641.1|DR332641
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036883|gb|DR332638.1|DR332638
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036875|gb|DR332630.1|DR332630
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036881|gb|DR332636.1|DR332636
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036876|gb|DR332631.1|DR332631
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|125278335|gb|EL292420.1|EL292420
EST:     CTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAAGAAGATTCTGCAGCTCCTGCGTT
genomic: CTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAA-GAAGATTCTGCAGCTCCTGCGTT
EST: gi|164100547|gb|ES122672.1|ES122672
EST:     CTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAA-CAAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: CTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036880|gb|DR332635.1|DR332635
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036879|gb|DR332634.1|DR332634
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036882|gb|DR332637.1|DR332637
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|164006836|gb|ES067520.1|ES067520
EST:     TGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036873|gb|DR332628.1|DR332628
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036877|gb|DR332632.1|DR332632
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036878|gb|DR332633.1|DR332633
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|86036874|gb|DR332629.1|DR332629
EST:     TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: TTCTACGTTGACCCTGAGGCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
EST: gi|124968135|gb|EL042110.1|EL042110
EST:     GCTAAGTTGCTCTTTATCATTCGTATCCGTGG                         TATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT
genomic: GCTAAGTTGCTCTTTATCATTCGTATCCGTGGgtatgtgcct ... tcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttgttgcatatagattctgttttttatttacgtgattgtttgtcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG
          atatagattctgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcctattatttgtgtgttacataagttgttgcatatagattctgttttttatttacgtgattgtttgtcatttgcagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC