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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtctcattgaaagtcaaatgttgctatgttgcaatcttgtaaaaatctgagtaatattgtgttgtgtgttaaacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAAGGTTGTTAGATGCGAGCCACCGTGATCTAAGGAGAGCAAGAGCAGCAGC

Basic information

species Arabidopsis thaliana
transcript AT1G12900.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G28240.1 (Glycine max), 3'ss of exon 4
------------gtaagcgtctcattgaaagtcaaatgttgctatgttgcaatcttgtaaaaatctgagtaatattgtgttgtgtgttaaact-tgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAAGGTTGTTAGATGCGAGCCACCGTGATCTAAGGAGAGCAAGAGCAGCAGC
             |    |    |||  |    || |  ||  | |     ||| | |      ||  | |      ||     ||  || |  ||  ||| ||||| |||||||| ||||| || |||||||| ||||| |||||||||||| |  | ||||||||||||||||| || ||| | ||||| ||||||||
ctaaaatgacttatgcatgcaatatttgagactaatttatgtgaagaaaagatcatattctctactatgcatgccaatggaaaatgacaatccatgacagGTATCATCAAGGGTACCATGACCACCACTCACTCCTACACCGGTGACCAAAGGCTTCTTGATGCGAGCCACCGTGACCTGAGGCGTGCAAGGGCAGCAGC

upper sequence: AT1G12900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0150g00500.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaagcgtctcattga---aagtcaaatgttgctatgttgcaatcttgtaaaaatctgagtaatattgtgttgtgtgttaaacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAAGGTTGTTAGATGCGAGCCACCGTGATCTAAGGAGAGCAAGAGCAGCAGC
          ||     ||||| |   || | ||||  |   ||     |  |   | |  ||||   ||  | | |     |||||  |  || |||| |||||||||||||||||||| || |||||||| |||||||| ||||| ||  | || ||||| |||||||| |  || |||   |   | || || | 
gtaattcatcaaatcattcatttactcaatttaaatcctataatacaatatacaaatcatcatcttcatatgaatatcaatggtgttccatatgatagGAATCATAAAGGGTACAATGACCACCACTCACTCTTACACTGGCGACCAGAGACTTTTTGATGCAAGCCACCGGGTCCTCAGGCCTGTGCGTGCTGCTGT
















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|125113705|gb|EL164426.1|EL164426
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATAGAACAACTACTCACTCATACACTGGTGA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAAT-GA-CAACTACTCACTCATACACTGGTGA
EST: gi|116451131|gb|EG493723.1|EG493723
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124793224|gb|EH882903.1|EH882903
EST:     CTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAAGAAAATTTG                         GGATCATAAAGGGTACAATGACAACT
genomic: CTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCA-GAAA-TTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACT
EST: gi|116442534|gb|EG485126.1|EG485126
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124732563|gb|EH823965.1|EH823965
EST:     ACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAAATTTG                         GGATCATAAAGGGTACAATGACAACT
genomic: ACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAA-TTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACT
EST: gi|125248771|gb|EL262856.1|EL262856
EST:     CTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATAC
genomic: CTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATAC
EST: gi|124754250|gb|EH844380.1|EH844380
EST:     GTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: GTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124793900|gb|EH883579.1|EH883579
EST:     ACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAAATTTG                         GGATCATAAAGGGTACAATGACAACTAC
genomic: ACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAA-TTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTAC
EST: gi|116399242|gb|EG441834.1|EG441834
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATATACTGGTGACCAAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124943899|gb|EL020050.1|EL020050
EST:     TTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|116408015|gb|EG450607.1|EG450607
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124779297|gb|EH869240.1|EH869240
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGG
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGG
EST: gi|125182352|gb|EL197883.1|EL197883
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GN-TCATAAAGGGTACAATGACAACTACTCACTCATAC
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATAC
EST: gi|125219382|gb|EL233467.1|EL233467
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACC
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACC
EST: gi|116473085|gb|EG515677.1|EG515677
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCA
EST: gi|124965493|gb|EL039677.1|EL039677
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         G-ATCGTAAAGGGTACAATG
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATG
EST: gi|124962499|gb|EL036920.1|EL036920
EST:     TCCATTCGTCAAGGTTCTTGACCAAAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124746794|gb|EH837094.1|EH837094
EST:     CTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATAC
genomic: CTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATAC
EST: gi|125301418|gb|EL315503.1|EL315503
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGAC
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGAC
EST: gi|164022420|gb|ES117361.1|ES117361
EST:     GTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: GTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124823750|gb|EH908616.1|EH908616
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCA
EST: gi|125244786|gb|EL258871.1|EL258871
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAA
EST: gi|125007892|gb|EL080161.1|EL080161
EST:     TGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACTAACTACTCACTCATACACTGGTGACCAA
genomic: TGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGAC-AACTACTCACTCATACACTGGTGACCAA
EST: gi|124892363|gb|EH971265.1|EH971265
EST:     AAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: AAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|116408023|gb|EG450615.1|EG450615
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124709043|gb|EH800445.1|EH800445
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAA
EST: gi|124951363|gb|EL026740.1|EL026740
EST:     TGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|125218814|gb|EL232898.1|EL232898
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCA
EST: gi|125080602|gb|EL142142.1|EL142142
EST:     ACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: ACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|125220122|gb|EL234207.1|EL234207
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACA
EST: gi|124886538|gb|EH965440.1|EH965440
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACT
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACT
EST: gi|124993602|gb|EL065871.1|EL065871
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATAC
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATAC
EST: gi|124916277|gb|EH990151.1|EH990151
EST:     ACTAACTGTCTCGCTCCATTCGTCAAGGTTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATAC
genomic: ACTAACTGTCTCGCTCCATTCGTCAAGG-TTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATAC
EST: gi|124845022|gb|EH929459.1|EH929459
EST:     ACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAAATTTG                         GGATCATAAAGGGTACAATGACAACTA
genomic: ACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAA-TTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTA
EST: gi|86081325|gb|DR377082.1|DR377082
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
EST: gi|124849662|gb|EH934099.1|EH934099
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGAACAACTACTCACTCATACACTGGTGA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGA-CAACTACTCACTCATACACTGGTGA
EST: gi|125207327|gb|EL222281.1|EL222281
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCAATAAAGGGTACAATGACAACTACTCACTCA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCA-TAAAGGGTACAATGACAACTACTCACTCA
EST: gi|125206531|gb|EL221485.1|EL221485
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAA
EST: gi|116473086|gb|EG515678.1|EG515678
EST:     TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTG                         GGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA
genomic: TACTACTAACTGTCTCGCTCCATTCGTCAAGGTTCTTGACCAGAAATTTGgtaagcgtct ... aacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcaatcttgtaaaaatctgagtaatattgtgttgtgtgttaaacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAAGGTTGTTAGATGCGAGCCACCGTGATCTAAGGAGAGCAAGAGCAGCAGC
      aatcttgtaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgtctcattgaaagtcaaatgttgctatgttgcaatcttgtaaaaatctgagtaatattgtgttgtgtgttaaacttgttagGGATCATAAAGGGTACAATGACAACTACTCACTCATACACTGGTGACCAAAGGTTGTTAGATGCGAGCCACCGTGATCTAAGGAGAGCAAGAGCAGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG