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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttcgtttcttgtaactcttcttgagattgtctgtagttctaaaactcgattttggatctaattgttgctcatcttcgattggattgagttggatcattgaattgatttgattattagaaagtttgtaacttggagctaagaaagctgattcctttttcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTGAGAGTGGTTTCATTAGAGGAGCAGCAATTGGAGCCATTTCGGGAGCTGT

Basic information

species Arabidopsis thaliana
transcript AT2G17730.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17730.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08540.1 (Glycine max), 3'ss of exon 1
gtttgttttcgtttcttgtaactcttcttgagattgtctgtagttctaaaactcgattttggatctaattgttgctcatcttcgattggattgagttggatcattgaattgatttgattattagaaagtttgtaacttggagctaagaaagctgattcctttttcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTGAGAGTGGTTTCATTAGAGGAGCAGCAATTGGAGCCATTTCGGGAGCTGT
                                                        |      | |  ||  || |  ||||  ||                |    | || ||| |  ||||  | || ||     ||        || | || ||   | |||   | |||| ||||| ||| | |||||  | || |||||||||||||| ||||||||||||||||| |||||| |||| || ||  |||| ||||| || ||||||||
--------------------------------------------------------tccaaagtttggttaatgtttttcttatatcc------------ctaccctagtgttttaaccatta--aggtgtggtgtgtgctttgtttaaggttgtttttgtcttc---tgcagTTGGCACTTTGTTGGGGGCTTTGACTGGAGCTTTGATAGGACAAGAAACTGAGAGTGGCTTCATTCGAGGGGCTGCTGTTGGTGCCATATCAGGAGCTGT

upper sequence: AT2G17730.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36760.1 (Glycine max), 3'ss of exon 2
gtttgttttcgtttcttgtaactcttcttgagattgtctgtagttctaaaactcgattttggatctaattgttgctcatcttcgattggattgagttg-gatcattgaattg----atttgattattagaaagtttgtaacttggagctaagaaagctgattcctttttcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTGAGAGTGGTTTCATTAGAGGAGCAGCAATTGGAGCCATTTCGGGAGCTGT
                                                                        ||||  ||||| |||   | | |||   | |||| || ||     | || || ||  || |    | | ||    ||||      || |   ||| ||   | |||| ||||| ||| | |||||  | || |||||||||||||| ||||||||||||||||| |||||| |||| || ||  |||| ||||| || ||||| ||
----------------------------------------------------------------------aatgcttttcttctattacctagtgttttaaacattaaagtgtggtgtgtgctttttttaaggacaatgagtt----ctaatg----tgttgtttttgtctgctgcagTTGGCACTTTGTTGGGGGCTTTGACTGGAGCTTTGATAGGACAAGAAACTGAGAGTGGCTTCATTCGAGGGGCTGCTGTTGGTGCCATATCAGGAGCCGT

upper sequence: AT2G17730.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G05000.1 (Glycine max), 3'ss of exon 1
gtttgttttcgtttcttgtaactcttcttgagattgtctgtagttctaaaactcgattttggatctaattgttgctcatcttcgattggattgagttggatcattgaattgatttgattattagaaagtttgtaact--tggagctaagaaagctgattcctttttcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTGAGAGTGGTTTCATTAGAGGAGCAGCAATTGGAGCCATTTCGGGAGCTGT
                                                                  ||  |||  |  ||||    |   ||  |||      ||||| |      | | | | ||  ||||   ||  |   | | |      || ||  | |   || | |||| ||||| ||| | |||||  | || ||||| |||||||| ||||| || ||||||||||||||| |||| || || || || ||||| || ||||||||
-----------------------------------------------------------------caaaggttttttttctttttataatttttgtt------ttgaaatt-ccaaactgtgacaatatttgaggctaataaggtttaatggattgtttgttat---atttgcagTTGGCACTTTGTTGGGGGCTATGACTGGAGCCTTGATAGGCCAAGAGACAGAGAGTGGTTTCATTCGAGGGGCCGCTATAGGTGCCATATCAGGAGCTGT

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|86056628|gb|DR352385.1|DR352385
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056626|gb|DR352383.1|DR352383
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056631|gb|DR352388.1|DR352388
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056625|gb|DR352382.1|DR352382
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056624|gb|DR352381.1|DR352381
EST:     TGTTTTGGGTA-CATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056632|gb|DR352389.1|DR352389
EST:     TGTTTTGGGTA-CATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056623|gb|DR352380.1|DR352380
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056633|gb|DR352390.1|DR352390
EST:     TGTTTTGGGTAC-ATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGCGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACT
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTG-GGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACT
EST: gi|86056627|gb|DR352384.1|DR352384
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056622|gb|DR352379.1|DR352379
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
EST: gi|86056630|gb|DR352387.1|DR352387
EST:     TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAG                         TGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG
genomic: TGTTTTGGGTACCATTATCTCCGCGATCTTGACCTTCTTCTTCGCACTAGgtttgttttc ... tcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattagaaagtttgtaacttggagctaagaaagctgattcctttttcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTGAGAGTGGTTTCATTAGAGGAGCAGCAATTGGAGCCATTTCGGGAGCTGT
                                     ttcctttttcatgttc  CT-rich tract
                                         tttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttttcgtttcttgtaactcttcttgagattgtctgtagttctaaaactcgattttggatctaattgttgctcatcttcgattggattgagttggatcattgaattgatttgattattagaaagtttgtaacttggagctaagaaagctgattcctttttcatgttcagTGGGCACATTGCTAGGGGCACTTACAGGAGCTTTGATAGGTCAAGAAACTGAGAGTGGTTTCATTAGAGGAGCAGCAATTGGAGCCATTTCGGGAGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT