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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctcattcatcggttgcttatctttgaattacaataaagatagagaattgatgatcttccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG

Basic information

species Arabidopsis thaliana
transcript AT2G40590.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
gtactctcattcatcg--gttgcttatctttgaattacaataaagatagagaattgatgatcttccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
|||     ||  || |   ||| |||| ||||||      |    ||     || | ||   |    |||||||||||     ||||||||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||  ||||||||||||||||||||||||||||||||
gtagaag-atctattgccattgtttatttttgaagcttcttcttcatctc--atcgttgga-tcatgttgttgtttgt-----agACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
---------gtactctcattcatcggttgcttatctttgaattacaataaagatagagaattgatgatcttccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
          |  ||| |||| |||||| |   |  ||  || ||  |     |      ||||  ||||   |||||||||||| ||| |||| |||||||| |||||||| ||  | ||||| |||  | | || || |||||    ||| |||||||||||||||||||||||||||| |||
gttcgagatctgttcttattc-tcggtttcc-gtaattccataaccttcttcttctttccttga--atctcgtattgttgtttgt-ttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G14950.1 (Glycine max), 3'ss of exon 1
---------gtactctcattcatcggttgcttatctttgaattacaataaagatagagaattgatgatcttccat-----tgttgtttgtgt-tgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
          ||    ||||  ||  | | || | ||    || ||  ||          || || ||||   ||     |||||||| ||| |||||||||| ||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||  ||||||||||||||||||||||||| ||||||
gtagaagatctatcgccattgttccttcgttttttttcttttttcacaaacttcttcttcttcatcatctcatatcttcttgttgtttttgtctgcagACTTTTAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGTCCTAAG

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 3'ss of exon 1
gtactctcattcatcggttgcttatctttgaattacaataaagatagagaattgatgatcttccattgttgtttgtgtt---gcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
||    |  | |         | |  ||| |||     |    ||      |    ||| ||   ||| |  |||||||   |||||| |||||||||||||| |||||  | |||||||||  | | || ||||||||    ||  | ||||||||||| ||||||||||||||||||
gtgaggttttcctcgaaaatttcacttttcaatcttgcttgctatcatttctcaccgattttt--ttggtaattgtgtttttgcagACGTTCAAGCGAAGGAATGGTGGTCGCAACAAGCACGGCCGCGGCCACGTCAAGTTCATTCGCTGCTCCAACTGTGGCAAATGCTGCCCTAAG

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|164065356|gb|EL977117.1|EL977117
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCA-GCGAAGG
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGG
EST: gi|86018764|gb|DR314510.1|DR314510
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018765|gb|DR314511.1|DR314511
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAAAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018763|gb|DR314509.1|DR314509
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018762|gb|DR314508.1|DR314508
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018768|gb|DR314514.1|DR314514
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAAAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018759|gb|DR314505.1|DR314505
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018770|gb|DR314516.1|DR314516
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018767|gb|DR314513.1|DR314513
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAAAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018760|gb|DR314506.1|DR314506
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAAAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018757|gb|DR314503.1|DR314503
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018758|gb|DR314504.1|DR314504
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018761|gb|DR314507.1|DR314507
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018766|gb|DR314512.1|DR314512
EST:     TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TTAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAAAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86018769|gb|DR314515.1|DR314515
EST:     TAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCAMCAGATG                         ACTTTCAAGCG-AGGAACGGTGGGAGG-ACAAGCACAACAGAGGACACGT
genomic: TAAGTCCATCGACATCTGGAGAGTGAGAAGAGAGGAATAGCCA-AAGATGgtactctcat ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattacaataaagatagagaattgatgatcttccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
                     aattgat  putative branch site (score: 4)
        aataaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactctcattcatcggttgcttatctttgaattacaataaagatagagaattgatgatcttccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC