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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaataaactattaacgttttcatcactaaataaatcggaatttaaacccatttttagcaagagaaaacatgttcatgtttgttacaatatatttgttgttctattttggatttaaaccttctccagtgaaaattatataatacaatacctttgagatccctaaatctttgctttaatttattctatag

Basic information

species Arabidopsis thaliana
transcript AT5G50950.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50950.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 16
AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaata-aactattaacgttttcatcactaaataaatcggaatttaa--acccatttttagcaagagaaaacatgttcatgtttgttacaatatatttgttgttctattttggatttaaaccttctccagtgaaaattatataatacaatacctttgagatccctaaatctttgctttaatttattctatag
|||||||||||||||||||||||||| || || || | ||| |||||||||||| ||||||| ||||| |  | |  |  ||||   ||| |  | | |  |  ||  |   |  ||    |    ||   |   ||   | |||| ||    |  |   |||| ||||                                                                                             
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAGgtgattattccatttattttagttgttttgattcga--aactgatgtgcaatggtctgcgttagccttaaggtgatatgtgcaaacataatttcatat-tttg---------------------------------------------------------------------------------------------

upper sequence: AT5G50950.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 16
AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaaca---ataaactattaacgttttcatca--ctaaataaatcggaatttaaacccatttttagcaagagaaaacatgttcatgtttgttacaatatatttgttgttctattttggatttaaaccttctccagtgaaaattatataatacaatacctttgagatccctaaatctttgctttaatttattctatag
|||||||||||||||||||||||||| || || || | ||| ||||||||||||  ||| || ||||| | |     | |  ||||    ||| | |    ||   |   | |    |||    |  | |||||   ||   || ||  ||||||       |||| || |                                                                                             
AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAGgtgatctttcgttacttatttcactttgccttggccttgctctgtggtgtattacgtgctatcttagctt-aggtgacttgcgcatgtt------gatatcttggcc-------------------------------------------------------------------------------------------
















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|124730032|gb|EH821434.1|EH821434
EST:     ACAAAGAAGGATGCACATTAAAG                         CACGCTAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCT
genomic: ACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGC-AGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCT
EST: gi|86080103|gb|DR375860.1|DR375860
EST:     ATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
genomic: ATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
EST: gi|116428257|gb|EG470849.1|EG470849
EST:     ATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
genomic: ATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
EST: gi|124949085|gb|EL024749.1|EL024749
EST:     AGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
genomic: AGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
EST: gi|86075192|gb|DR370949.1|DR370949
EST:     ATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
genomic: ATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
EST: gi|124708829|gb|EH800231.1|EH800231
EST:     TGCTGCAGCTAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCGG
genomic: TGCTGCAGC-AGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCGG
EST: gi|124929064|gb|EL006647.1|EL006647
EST:     AGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
genomic: AGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
EST: gi|125217294|gb|EL231377.1|EL231377
EST:     ACAAAGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
genomic: ACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCGGAAGAGTTTGATACTCTT
EST: gi|125048445|gb|EL120714.1|EL120714
EST:     CACAAAGAAGGATGCACATTAAAG                         CACGCAGCTATGAAGTTAGGTGTTCTTACTTCG
genomic: CACAAAGAAGGATGCACATTAAAGgtaaacaata ... tattctatagCACGCAGCTATGAAGTTAGGTGTTCTTACTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGgtaaacaataaactattaacgttttcatcactaaataaatcggaatttaaacccatttttagcaagagaaaacatgttcatgtttgttacaatatatttgttgttctattttggatttaaaccttctccagtgaaaattatataatacaatacctttgagatccctaaatctttgctttaatttattctatag

- - - - - - - - ATGCTG
- - - - - - - -  TGCTGC
- - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AGGATG