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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacaagtgtcaatcatatgtcaattttaaagagaatgatagttattgagtttgtttgaccaatcatgatacggttgttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G20693.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20693.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G834758_T01 (Zea mays), 3'ss of exon 5
----------------------------------------gtataacaagtgtcaatcatatgtcaattttaaagagaatgatagttattgagt------ttgtttgacca-atca-------tgatacggttgttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG
                                        |||||   | ||    |  |  |||| || |  | | |   ||  ||| |||        |||||||  || | ||       | | | || |  ||  | |||||||||      |||| || ||||| |||||||||||   ||| ||||||||||||||||||||||  |                 
gtagggaaactgatgcttcaattgcgttgttacttaatgtgtatatagactgctcctgctg-gtcatttattcaaatacgtatgcttactgaaccatgtgttgtttgttcagAGCACTGCAGCTAAGAAGGCTCCTGCCA-AGGAGGAAGAGGAGGAAGATGAAGAGGAGTCTGACAAGTCCAAGTCGGAGGTCAATGACGAGGATGATGAAG-----------------
















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|164148015|gb|ES028283.1|ES028283
EST:     GTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAG
genomic: GTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAG
EST: gi|124937770|gb|EL014478.1|EL014478
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGT
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGT
EST: gi|164173814|gb|ES054557.1|ES054557
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGATGA
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGA
EST: gi|125030413|gb|EL102682.1|EL102682
EST:     TAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGTAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGT
genomic: TAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAG-AAGATGAGGAATCTGACAAGTCAGTGTCAGAGGT
EST: gi|116400368|gb|EG442960.1|EG442960
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGA
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGA
EST: gi|124777386|gb|EH867329.1|EH867329
EST:     AACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTC
genomic: AACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTC
EST: gi|125299616|gb|EL313701.1|EL313701
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAG
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAG
EST: gi|164128414|gb|ES207446.1|ES207446
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGG-CCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGG
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGG
EST: gi|125232624|gb|EL246709.1|EL246709
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGA
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGA
EST: gi|124991886|gb|EL064155.1|EL064155
EST:     AAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGATGAGGAAT
genomic: AAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAAT
EST: gi|164186858|gb|ES210970.1|ES210970
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGG
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGG
EST: gi|164230474|gb|ES155417.1|ES155417
EST:     AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTG                         GAGGAAGGTCCAAAAGAAGGTGAGGAATCTGACAAG
genomic: AACGCAAGGTTGAATATGAGAAGAACATTAAAGCTTACAACAAGAAACTGgtataacaag ... gttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaatgatagttattgagtttgtttgaccaatcatgatacggttgttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG
                      gtttgac  putative branch site (score: 4)
       atagttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataacaagtgtcaatcatatgtcaattttaaagagaatgatagttattgagtttgtttgaccaatcatgatacggttgttgttacagGAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA