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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtctctgattctgaatcgttcttgtagtgatttgatttatcatataagcgtagaagaacaatttgtgtttagttgaatttgatttttgttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGAGTGAATTGTCCGTTTTACTTTAAGATTGGTGCTTGTCGTCACGGTGACC

Basic information

species Arabidopsis thaliana
transcript AT5G42820.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g47750.1 (Oryza sativa), 3'ss of exon 3
tcgtctctgattctgaatcgttcttgtagtgatttgatttatcatataa-gcgtagaagaacaattt---gtgtttagttgaatttgatttttgt-tatgtttagGTGAGAATGGCAGAGCATTTAGCTTCA------ATCTTTGGTACTGAAAAGGATAGAGT----GAAT---TGTC--CGTTTTACTTTAA----GATTGGTGCTTGTCGTCACGGTGACC--------------
   ||  ||||| |||||| |    | ||   || | || |  || |    |  ||||  | ||  |    ||   | || | ||  |  || |    ||      || | ||  | | ||  ||  |||||        |     ||     ||   | | ||    |||    | ||  ||   |  | | |    |   || | |  |  ||| ||  | |              
-gttcgttgattttgaatcatggcag-agcacttagcttcaatatttggtacagagaaagataaggtcaactgcccattttacttcaagattggggcttgccgtcatggggat--cggtgctcttgtcttcataacagGCCCACCATATCACCAACTGTTGTGTTTGCGAACATGTATCAGCGCCCTGATATGATCACGCCCGGGGTTGATGCTCAAGGCCAGCCGATAGATCCCCGC

upper sequence: AT5G42820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G031827_T02 (Zea mays), 3'ss of exon 1
-------tcgtctctgattctgaatcgtt--cttgtagtgatttgattt-atcatataagcgtagaagaacaatttgtgtttagttgaatttgatttttgtta-tgtttagGTGAGA--ATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGAGTGAATTGTCCGTTTTACTTTAAGATTGGTGCTTGTCGTCACGGTGACC
       | ||   ||||       | |    || ||     |  |||| | | ||||    | |||||  |   | |  ||  ||    ||||   |||| | | |  | ||   |  ||||| ||||| || ||||| ||||||||||| || ||||| || || || || || |||||||| |||||||| ||||||||||         
atccccatggttcttgataacaggccatgagtttataccccctccatttcaccttata----ttgaagatgatactattcttgcttatgcttgaaggttgtcagTCTGCAAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGCTTGTCGTC---------
















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|86065755|gb|DR361512.1|DR361512
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTAG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065758|gb|DR361515.1|DR361515
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065761|gb|DR361518.1|DR361518
EST:     ACCTCCTCGTCGGCGATAGSTTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065753|gb|DR361510.1|DR361510
EST:     ACCTCCTCGTCGGCGATRGSTTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065757|gb|DR361514.1|DR361514
EST:     ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065763|gb|DR361520.1|DR361520
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTAG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065751|gb|DR361508.1|DR361508
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065754|gb|DR361511.1|DR361511
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065756|gb|DR361513.1|DR361513
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065762|gb|DR361519.1|DR361519
EST:     ACCTCCTCGTCGGCGATAGSTTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065764|gb|DR361521.1|DR361521
EST:     ACCTCCTCGTCGGCGATAACTTCTCTTCCACTAAAAGAAAATCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065752|gb|DR361509.1|DR361509
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065759|gb|DR361516.1|DR361516
EST:     TTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: TTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065765|gb|DR361522.1|DR361522
EST:     ACCTCCTCGTCGGCGATA-STTCTCTTCCACTAAAAGAAAACCCTCTTCG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: ACCTCCTCGTCGGCGATAGCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
EST: gi|86065760|gb|DR361517.1|DR361517
EST:     CCTCCTCGTCGGCGATASG-TTCTCTTCCACTAAAAGAAAACCCTCTTSG                         GTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA
genomic: CCTCCTCGTCGGCGATA-GCTTCTCTTCCACTAAAAGAAAATCCTCTTCGgtattcttct ... ttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagcgtagaagaacaatttgtgtttagttgaatttgatttttgttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGAGTGAATTGTCCGTTTTACTTTAAGATTGGTGCTTGTCGTCACGGTGACC
                                 atttgat  putative branch site (score: 5)
                                       tttttgtt  CT-rich tract
                                aatttgatttttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgtctctgattctgaatcgttcttgtagtgatttgatttatcatataagcgtagaagaacaatttgtgtttagttgaatttgatttttgttatgtttagGTGAGAATGGCAGAGCATTTAGCTTCAATCTTTGGTACTGAAAAGGATAGAGTGAATTGTCCGTTTTACTTTAAGATTGGTGCTTGTCGTCACGGTGACC

- gtctctg
- - - - - - ctgaatc
- - - - - - - - - - - - - - - gatttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - agaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttag