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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttcaatccgtatttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G31610.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaa--tgagtctcttatctaccat-ttagtgagtaagtataccggctttgtctaatcttgttggttc-aatccgtatttgcag
|||||| ||||||||||||||||| || |||||| |||| |||||| | ||   |||    || || ||  |||| || ||||||||| | || |||||||| ||      ||    |  |  ||   ||  || ||  ||  |   | |    ||||    |  | |  | |   |   | | | ||| |||
TGCTAAATCCATGAAGTTCAAGGACGGATACATGATTTCTTCTGGTTATCCTGTTAACTTGTATATTGACTCTGCTGTTAGACATGTTCTTCTGAGACAGgtttgtacataaaatccatccgtttgaataaaatgttgctgtctccttgtgatagcttgaatttttttcttagaagctgcttcttgttttcag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G093902_T02 (Zea mays), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttcta--atgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttcaatccgtatttgcag
||||||||| ||||||||||||||||| |||||| |||| |||||||| ||    ||   |||||| ||| | || |||||||||||| |  | |||||||| || |   |   || ||    |    ||  ||  |   |   |  | |   ||| |   ||||  |  | ||| | |  |  |  |   
TGCTAAGTCTATGAAGTTCAAGGATGGGTACATGATTTCTTCTGGTCATCCTGTCAACCTATACATTGATTCAGCTGTGAGACATGTTCTATTGAGACAGgtttggtgcttggtatcagatgttatcttattatgcaaacatataacaaaatagctgttagtaatact-ctagttgacttggcttcag---

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttcaatccgtatttgcag-------------------------------------------------
 || ||||||||||| ||||||||||| || ||| |||| ||||| ||||||   ||||| ||||| ||  ||||||||||||||||  | || |||||||| || ||| | ||   ||     |     ||  | |   |      ||  |  || ||  || ||||||| ||| |   | | | ||                                                  
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaatttcttttagcactaggattttc--atgttgttggctcattttctttcttcatggattgatggtgctaaatgctaattgattccttactgtcttatatatag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA16G33230.1 (Glycine max), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctt-----tctaatg---------agtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttcaatccgtatttgcag----------------------------
 || || |||||||| ||||||||||| |||||| | || ||||| ||||||   ||||| ||||| ||  ||||||||||||||||  | || |||||||| |||||     ||| ||          ||| | |  |   ||| | ||    |   |  |   |  |  | |  | || ||  |||||   | |      |                            
AGCCAAATCCATGAAATTCAAGGATGGGTACATGATCTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTCCTCCTAAGACAGgtttgcttctatttctcatattacatgatagtttttctttcgccact-aggattttcatgcatttggctcattttctatttttatttcaacatggaaagttggtgctaatcactattttcctgtcttacag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G28440.1 (Glycine max), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaatgagtctcttatcta-ccatttagtgagtaagtataccggctttg---tctaatcttgttggttcaatccgtatttgcag------------------------------------------------
 || ||||||||||| ||||||||||| |||||| |||| ||||| |||||    ||||| ||||| ||  | ||||||||||||||  | || |||||||| || ||| |  |   | |  ||  || |||  |  |   |     | | |   | |   | | || ||||||| ||| |   | | |  |                                                 
AGCCAAGTCCATGAAATTCAAGGATGGATACATGATTTCTTCTGGACAACCTGTCAAGGATTACATTGACTCAGCAGTGAGACATGTGCTACTAAGACAGgtttgttttttttttttttttctacatagccacctgattgattttctttcagcactaggattttcatgttgttggctcattttttttcttaatggattgatgttgctaaatgcaaaaagatttttcttcattgtcctatag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G21190.1 (Glycine max), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttcaatccgtatttgcag-------------------------------
 || || || |||||||| ||||||||||||||| |||| ||||| |||||    || || ||||| ||  ||||||||||||||||  | || ||||||||    || ||  |     || ||  | |    || | | | |  ||    |  ||||  | || | ||| || |    | |                                      
AGCCAAATCTATGAAGTTTAAGGATGGTTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgttattttgcttctattcttcatacattcttgatact-atttatcatttttgggttgttgattcattttgttttacgatgaagagatgatgctaattgttattttgttgctgcctcatag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgc----tttctaatgagtctct-tatctaccatttagtga-gtaagtataccggct--ttgtctaatcttgttggttcaatccgtatttgcag---------------------
|||||||||||||||||||||||||||||||||| | ||||||||    ||    || || ||||||||   ||| ||  |||| ||| || |  | ||||||  |    |   | |||    ||  || || |  ||| ||     ||  |||  |  |  | |||     |       | |||| | | | |  |                     
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGGAGCCCTGTCAACGATTACATCGACAGTGCCGTCCGACACGTTATGTTGCGTCAGgtacacaagatgcttgatgtccgtcagtagctcctttttcgtactagaaagatattgattgatagtcggtgttcccgaagtgaatctgaagtggaggattactttggtatgtttacag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttc-------aatccgtatttgcag--------------------------------------------
 || ||||| ||||||||||||||||| |||||| ||||||| ||    ||    || || |||||||||  ||| || ||||| ||  || |  ||||||| ||      |   | ||  |  | | ||  |  ||| ||     | | |  ||   |||   |  ||| ||        ||  |   ||||||                                             
AGCCAAGTCTATGAAGTTCAAGGATGGCTACATGATTTCATCAGGAAGCCCCGTCAACGATTACATCGATAGTGCTGTCAGACACGTCATGTTACGACAGgtttgtcgagcagctattcagtggtgt-cctctctgtg-gtctccttgctgatttctcctacggtctttgttttcaagaaaaaatctcgtttgcaagttgtctgtaatgtatcttagaaatgtttcgttatttttttcag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtat--------gctttctaatgagtctcttatctaccatttagtgagt------aagtataccggctttgtct---aatcttgttggttcaatccgtatttgcag-----------------------------
||| |||||||||||||||||||| || |||||| | ||||||||    ||    || || ||||| |||  ||| || ||||| ||  || |  |||||||||        ||||| ||||     |  | || ||| || | |||||      || |||   |  ||  |     |  || |||  ||   |   || |   |                              
TGCAAAGTCCATGAAGTTCAAGGACGGATACATGATATCATCTGGAAGCCCTGTCAACGACTACATTGATAGTGCTGTAAGACACGTCATGTTGCGACAGgtattcttgacagctttttaatcttgttagtctcaaccgttcactgagtttcttcaattattgtgatttcattcggaaggctcgtttattagttttttactacgaatctcaggttttggatgtatgtttttgcag

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|86082133|gb|DR377892.1|DR377892
EST:     CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGA-CCTACGGGC
genomic: CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|116442865|gb|EG485457.1|EG485457
EST:     CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
genomic: CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|163998643|gb|ES146541.1|ES146541
EST:     ACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGG
genomic: ACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGG
EST: gi|164097466|gb|ES210885.1|ES210885
EST:     CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAAT
genomic: CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAAT
EST: gi|86080151|gb|DR375908.1|DR375908
EST:     CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACY-TACGGGC
genomic: CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|86079515|gb|DR375272.1|DR375272
EST:     CAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGNA-CCTACGGG
genomic: CAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGG-ACCCTACGGG
EST: gi|164238045|gb|ES052769.1|ES052769
EST:     GCTGCAGTGAGACATGTTTTGCTCAGACAGG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGG
genomic: GCTGCAGTGAGACATGTTTTGCTCAGACA-Ggtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGG
EST: gi|116410815|gb|EG453407.1|EG453407
EST:     CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
genomic: CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|125011112|gb|EL083381.1|EL083381
EST:     TGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
genomic: TGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|125003649|gb|EL075918.1|EL075918
EST:     GAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGG
genomic: GAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGG
EST: gi|125314247|gb|EL328332.1|EL328332
EST:     CTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
genomic: CTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|164095236|gb|ES185577.1|ES185577
EST:     CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTAGGGAATCAAGGTGAAGATCA
genomic: CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTT-GGGAATCAAGGTGAAGATCA
EST: gi|86076619|gb|DR372376.1|DR372376
EST:     CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGA-CCTACGGGC
genomic: CAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|124866390|gb|EH950827.1|EH950827
EST:     GCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
genomic: GCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|124934478|gb|EL011545.1|EL011545
EST:     ATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
genomic: ATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
EST: gi|124914405|gb|EH988279.1|EH988279
EST:     GATGCTGCAGTGAGACATGTTTTGCTCAGACAG                         GGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC
genomic: GATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttc ... gtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttcaatccgtatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG