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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagagctaattaataacactccaattcttgaaacattcattgcataagcaataacactctaatgactttgtggtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTTTGACATTTCTGTAGCAAAGT

Basic information

species Arabidopsis thaliana
transcript AT1G20020.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g01340.2 (Oryza sativa), 3'ss of exon 3
gtaagaagagcta-attaataacactccaattcttgaaac--attcattgcataagcaataacactctaatgactttgtggtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTTTGACATTTCTGTAGCAAAGT
       |  ||  | || ||   ||   | |||  |     ||||  | | |||  | |  |  |||    | | | |  ||  | |||| || |||||| |||| |||||||||||| |||||||| | ||||||||||| || |||||||||||||  | |    | ||  | |  |  |  ||   
-------gtactgtactagtacttcttttaatctccatctctattcgattcctaattactttctttcttgc-attatatactgtatgtagGCATCGACTGGCTTGACTACAAGAAGCAGCTGAAGAAGTCGGAGCAATGGAATGTGGAAGTCTACTGATGGATATATATATGTTAATAATTAATTAATCC

upper sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 7
gtaagaagagctaattaataacactccaattcttgaaacattca-----ttgcataag-caataacactctaatgactttgtggt---ggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGAT-CAAAAAGCCTTTGACATTTCTGTAGCAAAGT
|||   |  |||  | ||    ||     | | || |  ||| |      ||  |||  |  |  ||  ||||    |   ||||   | | ||||| || ||||||  |||||||||||||||  |||||||||  |||||||||||||| |||||||||| || |    |   ||   ||  |||||  |     
gtatatat-gcttctgaaccttacctttttgcatggataatttaagaatctgagtaattcttttgcatgctaaattttgcatggtatcgttgttagGAATCGACTGGGCTGATTACAAGAAGCAACTGAAGAAGGGCGAGCAATGGAACGTGGAAGTCTACTAATTCTTCCAATTTTCCTCACATCTGTTTCTTTT-

upper sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G059083_T04 (Zea mays), 3'ss of exon 6
------------gtaagaagagctaattaataacactccaattcttgaaacattcattgcataagcaataacactctaatgactttgtggtggtt-ttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTTTGACAT-TTCTGTAGCAAAGT
              || | || | | |   ||||  | |             ||  ||    |  ||   | |  ||| | ||             | ||| ||  ||||||| || |||||||||||| | ||||||   |||||||||||||| |||||||||||||  |  | ||||     | || |  |||  |  
cgttttttgcgctcaatatgaacaagtagctaacctttcttgctgcattggtttggttaatcacacacatatatactactcacgcatcatcatccgtcagGGATCAACTGGTTGGACTACAAGAAGCAGCTCAAGAAGAGCGAGCAATGGAACGTCGAAGTCTACTGAT-GATGATCCTTCATTGTATTGTTCAGCTCAAG

upper sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G059083_T05 (Zea mays), 3'ss of exon 2
-----------------------------------------gtaagaagagctaattaataacactccaattcttgaaacattcattgcataagcaataacactctaatgactttgtggtggtt-ttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTTTGACAT-TTCTGTAGCAAAGT
                                           || | || | | |   ||||  | |             ||  ||    |  ||   | |  ||| | ||             | ||| ||  ||||||| || |||||||||||| | ||||||   |||||||||||||| |||||||||||||  |  | ||||     | || |  |||  |  
gtaagttgtctgtcatctcgcttgtccttcgttttttgcgctcaatatgaacaagtagctaacctttcttgctgcattggtttggttaatcacacacatatatactactcacgcatcatcatccgtcagGGATCAACTGGTTGGACTACAAGAAGCAGCTCAAGAAGAGCGAGCAATGGAACGTCGAAGTCTACTGAT-GATGATCCTTCATTGTATTGTTCAGCTCAAG

upper sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G059083_T02 (Zea mays), 3'ss of exon 5
------------------------------------gtaagaagagctaattaataacactccaattcttgaaacattcattgcataagcaataacactctaatga-ctttgtggtggtt--ttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTTTGACAT-TTCTGTAGCAAAGT
                                    ||          ||  | || |   | || |   | ||| ||  ||||   |    |     | | || | | |  |  |  |   | ||| ||  ||||||| || |||||||||||| | ||||||   |||||||||||||| |||||||||||||  |  | ||||     | || |  |||  |  
gtaagctgtctgtcatcgctcttgtccttcgtttttgtgctcgatatgaacaagtagctagctaactaacgtaacctttcttgctgcattggtttggttatcatcatcatcatcatcatccgtcagGGATCAACTGGTTGGACTACAAGAAGCAGCTCAAGAAGAGCGAGCAATGGAACGTCGAAGTCTACTGAT-GATGATCCTTCATTGTATTGTTCAGCTCAAG

upper sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G059191_T01 (Zea mays), 3'ss of exon 6
--------------------------gtaagaagagctaattaataacac-tccaattcttgaaacattcattgca--taagcaataacactctaatgactttg-tggtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCT-TTGACATTTCTGTAGCAAAGT
                             | |  ||||||  | | |  | | ||||   ||   |||||   ||   |||  ||  || | |  | ||| ||  |  |    | ||| || |||||| |  | |||||||||||| | |||||||  |||||||||||||| || ||||||||||| |     |  |||||   |  | ||   |  
gtacgtcgtgcagtgccagtgcctggcctatactagctaaacattcatgcatgcaatgtctgttccattcccggcggctaactaaccac-caccgacgaccttaattattcgatcagGGATCGACTGGATGCAGTACAAGAAGCAGCTCAAGAAGGGCGAGCAATGGAACGTCGAGGTCTACTGATCCATCCTTCCGTTGACGACTGCGGAGATCAA-

upper sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G168143_T01 (Zea mays), 3'ss of exon 7
--gtaagaagagctaattaat--aacactccaattcttgaaacattcattgcataagcaataacactctaatgactttgtggt-------ggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTT-----TGACATTTC-TGTAGCAAAGT
   |    | |     | |||   |  ||  | |||      |  |   ||     ||    ||  | |  ||  | | | |          | | ||| || |||||||| || |||||||||||| |||||| || ||| |||||||| || || ||||||| | |    |   ||     ||||||||  ||| |      
gtatgcagataatctttcaatctgaacctttagttccaactgctcttgatggtggcgctgagactttgtgttgcatatattgcttgcttaaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG------

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|86074562|gb|DR370319.1|DR370319
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
EST: gi|124901573|gb|EH975653.1|EH975653
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTG
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTG
EST: gi|125320460|gb|EL334545.1|EL334545
EST:     AAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAG
genomic: AAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAG
EST: gi|125218218|gb|EL232301.1|EL232301
EST:     TTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
genomic: TTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
EST: gi|125306008|gb|EL320093.1|EL320093
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTG
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTG
EST: gi|125131527|gb|EL174104.1|EL174104
EST:     GATGACATTATGGTCTCATTGGCTTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
genomic: GATGACATTATGGTCTCATTGGC-TGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
EST: gi|125134862|gb|EL175506.1|EL175506
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTA
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTA
EST: gi|125257826|gb|EL271911.1|EL271911
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACT--TTTGATTACAAGAAG
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAG
EST: gi|86081707|gb|DR377464.1|DR377464
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
EST: gi|124832250|gb|EH916689.1|EH916689
EST:     GGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
genomic: GGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
EST: gi|124788301|gb|EH877980.1|EH877980
EST:     ATTATGGTCTCATTGGCTGCAAATTGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGG
genomic: ATTATGGTCTCATTGGCTGCAAA-TGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGG
EST: gi|124796170|gb|EH885849.1|EH885849
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAG
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAG
EST: gi|124747131|gb|EH837283.1|EH837283
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGA
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGA
EST: gi|124762072|gb|EH852202.1|EH852202
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGT
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGT
EST: gi|124983954|gb|EL056651.1|EL056651
EST:     ATTGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAG
genomic: A-TGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAG
EST: gi|124750192|gb|EH840322.1|EH840322
EST:     TTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
genomic: TTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
EST: gi|124936069|gb|EL013004.1|EL013004
EST:     AAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAG
genomic: AAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAG
EST: gi|125011134|gb|EL083403.1|EL083403
EST:     TTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
genomic: TTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGA
EST: gi|125190396|gb|EL205350.1|EL205350
EST:     ATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAAGAAGGCAGAGCAATGG
genomic: ATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAA-GAAGGCAGAGCAATGG
EST: gi|125280310|gb|EL294395.1|EL294395
EST:     AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACG                         GTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCA
genomic: AATGGAGAAAGGAATTGATGACATTATGGTCTCATTGGCTGCAAATGACGgtaagaagag ... gtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaacattcattgcataagcaataacactctaatgactttgtggtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTTTGACATTTCTGTAGCAAAGT
       attcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaagagctaattaataacactccaattcttgaaacattcattgcataagcaataacactctaatgactttgtggtggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTTTGACATTTCTGTAGCAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG