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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctactgcttctttttcttgtcctgtattcagtcttatgggagttattgcacaataatcttctttttatcag

Basic information

species Arabidopsis thaliana
transcript AT5G57655.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G081682_T01 (Zea mays), 5'ss of exon 11
TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtc--tactgcttctttttcttgtcctgtattcagtcttatggg--agttattgcacaataatcttctttttatcag-------------------------------------
                                                || |  ||  || ||||||||||||  ||||||||||||||||||||||| ||||| ||  | | | |||||| |  |  || ||    |     ||      |  || |  || |  ||||   | |  ||                                      
------------------------------------------------GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagtcccgtttctttatgattacccgttccaatgtccataactttgacatagtgcattg-tctttactatgccaatttggtgacagaactgaaattttattatgtatttcag

upper sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 11
TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctactgcttctttttcttgtcctgtattcagtcttatgggagttattgcacaataatcttctttttatcag--------------------------------------
                                                || |  ||  || ||||||||||||  ||||||||||||||||||||||| ||||| ||      || | ||| |  | |    | || | |  |   |  | | ||| | |    |   |||||  |                                       
------------------------------------------------GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagtgttttttctttatgatacctgttccaatgtcctt--aactttggcatagtgcattgtcttttactatgccgatttggtgaaagaactaagattttgttatttcag

upper sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G313536_T01 (Zea mays), 5'ss of exon 10
TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtc--tactgcttctttttcttgtcctgtattcagtcttatggg--agttattgcacaataatcttctttttatcag-------------------------------------
                                                || |  ||  || ||||||||||||  ||||||||||||||||||||||| ||||| ||  | | | |||||| |  |  || ||    |     ||      |  || |  || |  ||||   | |  ||                                      
------------------------------------------------GCTAATTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagtcccgtttctttatgattacccgttccaatgtccataactttgacatagtgcattg-tctttactatgccaatttggtgacagaactaaaattttattatgtatttcag

upper sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G427620_T01 (Zea mays), 5'ss of exon 6
TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtc--tactgcttctttttcttgtcctgtattcagtcttatggg--agttattgcacaataatcttctttttatcag-------------------------------------
                                                || |  ||  || ||||||||||||  |||||||||||||||||||||||  |||| ||  | | | |||||| |  |  || ||    |     ||      |  || |  || |  ||||   | |  ||                                      
------------------------------------------------GCTAATTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACAgtaattcagtcccgtttctttatgattacccgttccaatgtccataactttgacatagtgcattg-tctttactatgccaatttggtgacagaactaaaattttattatgtatttcag

upper sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G544990_T01 (Zea mays), 5'ss of exon 10
TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtc--tactgcttctttttcttgtcctgtattcagtcttatggg--agttattgcacaataatcttctttttatcag-------------------------------------
                                                || |  ||  || |||||| |||||  ||||||||||||||||||||||| ||||| ||  | | | |||||| |  |  || ||    |     ||      |  || |  || |  ||||   | |  ||                                      
------------------------------------------------GCTAATTTTCTTCAAGCTGTTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagtcccgtttctttatgattacccgttccaatgtccataactttgacatagtgcattg-tctttactatgccaatttggtgacagaactaaaattttattatgtatttcag

upper sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA17G07380.1 (Glycine max), 5'ss of exon 11
TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtct-------actgcttctttttcttgtcctgtattcagtc---ttatgggagttat-tgcacaataatcttctttttatcag-------------
                                                || ||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| | |       | | |  || | |||     | |||  |      |||||  |  ||  ||     |  | ||||||| |||               
------------------------------------------------GCTAGGTTTTTTGAAGCTGCTGTTGCATACAAAAAGAAGATTGGATTCAATGgtaactttctgtagaattcccactatctctaccattttataaaactaaattatgaaacatagatgttttgtg-ttttcttttaatctctgtatgttactct

upper sequence: AT5G57655.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 5'ss of exon 11
----------------------------------------------------TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctactgcttctttttcttgtcctgtattcagtcttatgggagttattgcacaataatcttctttttatcag
                                                    ||||| || || |||||||| |||||||||||||||||||||||| | |     || || ||      | ||| |         |   ||   ||  |   || ||  |||  ||| |    | || |   |||  ||  | |   |    |   |                     
TACACATTATTTAGGTGGAGAAAACTATGTTTTCTGGGGTGGTCGAGAAGGTTATCAAACTCTATTGAACACAGATATGGGAAGAGAGCTTGATCATTTGgtacatttattggacatccgttttgtt---------attgttctcttttatattacgtgaactctttcctcccttggtacaaaatttggtactttaatatcggtattag--------------------

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|164236754|gb|ES021721.1|ES021721
EST:     CAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAG                         GCACGCTTTTAANCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTA
genomic: CAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctac ... tttttatcagGCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTA
EST: gi|164187066|gb|ES036346.1|ES036346
EST:     CAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAG                         GCACGCTTTTAANCGAGCCCAAGCCTCAAGAACCCACCAAGCACC
genomic: CAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctac ... tttttatcagGCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACC
EST: gi|163981175|gb|ES205251.1|ES205251
EST:     TTTGAAGCTGCTGTTGCTTACAAGAAGAAGTATTGGTATTCAAAG                         GCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTAT
genomic: TTTGAAGCTGCTGTTGCTTACAAGAAGAAG-ATTGG-ATTCAAAGgtaagtctac ... tttttatcagGCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTAT
EST: gi|86055232|gb|DR350989.1|DR350989
EST:     CAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAG                         GCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTATG
genomic: CAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctac ... tttttatcagGCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTATG
EST: gi|124705963|gb|EH797365.1|EH797365
EST:     AAGATTGGATTCAAAG                         GCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTATG
genomic: AAGATTGGATTCAAAGgtaagtctac ... tttttatcagGCACGCTTTTAATCGAGCCCAAGCCTCAAGAACCCACCAAGCACCAGTATG
EST: gi|164139107|gb|ES032253.1|ES032253
EST:     AGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAG                         GCACGCTTTTAATCGAGCCCAAGCC
genomic: AGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctac ... tttttatcagGCACGCTTTTAATCGAGCCCAAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCAGACACTCTTGAACACTGATATGGGAAGAGAGCTTGATCATCTAGCCAGGTTCTTTGAAGCTGCTGTTGCTTACAAGAAGAAGATTGGATTCAAAGgtaagtctactgcttctttttcttgtcctgtattcagtcttatgggagttattgcacaataatcttctttttatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG