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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagagaccaacactaaccagaaatctacatttgctattgttatgtttgtgcctgttttgtcttaacgatatttgcattgttttgtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAGCAGCAATATGGTTTTTGTTCTGCATCACTCCTTCTTTGAAGCCATGTTT

Basic information

species Arabidopsis thaliana
transcript AT5G28060.1
intron # 4
splice site 3'
intron type U2

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|125141785|gb|EL179286.1|EL179286
EST:     AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATA
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATA
EST: gi|125294412|gb|EL308497.1|EL308497
EST:     AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAG
EST: gi|124933481|gb|EL010634.1|EL010634
EST:     AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAGAAGTAAGACG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACG
EST: gi|116424160|gb|EG466752.1|EG466752
EST:     ATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
genomic: ATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
EST: gi|125030490|gb|EL102759.1|EL102759
EST:     GGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAAGGACGAAA
genomic: GGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGA-GGAC-AAA
EST: gi|125168664|gb|EL193193.1|EL193193
EST:     AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
EST: gi|164144262|gb|ES196463.1|ES196463
EST:     AGATCAAGGAGAGGAAGAACAGGGCTAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGAT
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGAT
EST: gi|124981058|gb|EL053952.1|EL053952
EST:     AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAG
EST: gi|86084565|gb|DR380324.1|DR380324
EST:     AGATCAAGGAGAGGAAAAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATGCCAAGAAGAAGTAAGACGTTTGAAGAGGACAGAAG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
EST: gi|86078425|gb|DR374182.1|DR374182
EST:     AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATGCCAAGAAGAAGTAAGACGTTTGAAGAGGACAGAAG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
EST: gi|116424161|gb|EG466753.1|EG466753
EST:     ATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
genomic: ATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
EST: gi|164033240|gb|ES112106.1|ES112106
EST:     AGATCAAGGAGAGGAAGAACAGGGCTAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTG
EST: gi|86081226|gb|DR376983.1|DR376983
EST:     AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATGCCAAGAAGAAGTAAGACGTTTGAAGAGGACAGAAG
genomic: AGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAG
EST: gi|124867524|gb|EH951961.1|EH951961
EST:     ATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG                         ACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAA
genomic: ATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagaga ... gtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgtttgtgcctgttttgtcttaacgatatttgcattgttttgtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAGCAGCAATATGGTTTTTGTTCTGCATCACTCCTTCTTTGAAGCCATGTTT
                     tcttaac  putative branch site (score: 2)
                                     attgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagagaccaacactaaccagaaatctacatttgctattgttatgtttgtgcctgttttgtcttaacgatatttgcattgttttgtgagtgtagACCAAGGCTGGTGATACCAAGAAGAAGTAAGACGTTTGAAGAGGACAAAAGCAGCAATATGGTTTTTGTTCTGCATCACTCCTTCTTTGAAGCCATGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC