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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTACTACTACCTGAGGAAGAAGGTGGCCTACGAGGCCATAGATCTCGACGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattgaaattgagcaatcaatcagtcagctcatctagctagccggccggagctagcaagcatgcaacagtgagatttagctgaagtttaaacatggtgattaatatttcatgtggtatatatacag

Basic information

species Oryza sativa
transcript LOC_Os06g33940.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G104074_T01 (Zea mays), 5'ss of exon 2
CTCTACTACTACCTGAGGAAGAAGGTGGCCTACGAGGCCATAGATCTCGACGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaa-attgaaattgagcaatcaatca-gtcagctcatctagctagccggccggagcta-gcaagcatgcaac-agtgagatttagctgaagtttaaacatggtgattaatatttcatgtggtatatatacag
|||||||||||||||||||| ||||| || || ||| |||||||||| || |||||||||||||| || ||||| ||||| |||||||||||||||||||||||| | |  |  |  | | | |   | | ||  | || | |   ||   | | |   |  |  |  |||| | ||  || |  | ||||  | | | ||                                 
CTCTACTACTACCTGAGGAAAAAGGTTGCTTATGAGCCCATAGATCTTGATGTCATAAGGGAGATTGATCTCAATAAGCTTGAGCCCTGGGATCTCAAAGgtaaataatagatatatgtatttatagatgccattttatttggtgtgcaaactgcaaacatacttgactgcagctagcaagctagatctga--tcttaccag--------------------------------

upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G041746_T01 (Zea mays), 5'ss of exon 2
CTCTACTACTACCTGAGGAAGAAGGTGGCCTACGAGGCCATAGATCTCGACGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattgaaattgagcaatcaatcagtcagctcatct------agctagccggccggagctagcaa-gcatgca---acagtgagatttagctgaagtttaaacatgg-------tgattaatatttc-atgtggtatatatacag-----------------------------------------------
||||||||||||||||||||||||||  |||| ||| |||||||||| || |||||||||||||| || |||||| |||| ||||| |||||||||||||||||   | ||||  |   ||  ||  ||||  |  | |      |||||||   |     || |  |   ||  |    ||| ||| |  | |||| |||   |  | |       | |||||| |||         | | | | |                                                
CTCTACTACTACCTGAGGAAGAAGGTTTCCTATGAGCCCATAGATCTTGATGTCATAAGGGAGATTGATCTCAACCAGCTTGAGCCATGGGATCTCAAAGgtaag--taaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcag

upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 5'ss of exon 1
CTCTACTACTACCTGAGGAAGAAGGTGGCCTACGAGGCCATAGATCTCGACGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattgaaattgagcaa--tcaatcagtcagctcatctagctagccggccggagctagcaagcatgcaacagtgagatttagctgaagtttaaaca----tggtgattaatatttcatgtggtat-----atatacag
       | || ||       || ||||     |||  |  ||   ||  | | ||   |||| | |||||||||||| ||||||||||||||||  |   |    |      ||| ||   ||| |       |  || |   |  |         | |   ||  |       |  |  || |  ||  | |  | |    || |  | ||| |||   | | | |      ||| |||
-------ATTATCTTTATGGCAAAGTGGGTA--GAGCGCGGAGTGATCAGC-TGATTCAGGAGTTGGACCTCAACAAGTTCGAGCCCTGGGATCTTCACCTTGTGCTGATgcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatactgatgatattcaatttttgtggcgatgtcaggggtatgcag

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|88362189|gb|CI608580.1|CI608580
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88354761|gb|CI614039.1|CI614039
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88364668|gb|CI612483.1|CI612483
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88390449|gb|CI607485.1|CI607485
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCACCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88393347|gb|CI618235.1|CI618235
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88328889|gb|CI646966.1|CI646966
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88340209|gb|CI652558.1|CI652558
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88377590|gb|CI605425.1|CI605425
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88420976|gb|CI620294.1|CI620294
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCACAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88351699|gb|CI617424.1|CI617424
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88422882|gb|CI615182.1|CI615182
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGC-
genomic: -GTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88351049|gb|CI620709.1|CI620709
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88392464|gb|CI612938.1|CI612938
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
EST: gi|88390496|gb|CI607532.1|CI607532
EST:     CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAG                         ATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC
genomic: CGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattga ... atatatacagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTACTACTACCTGAGGAAGAAGGTGGCCTACGAGGCCATAGATCTCGACGTCATAAGGGAGATCGACCTCAACAAGCTCGAGCCCTGGGATCTCAAAGgtaaaattgaaattgagcaatcaatcagtcagctcatctagctagccggccggagctagcaagcatgcaacagtgagatttagctgaagtttaaacatggtgattaatatttcatgtggtatatatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT