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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcgtgctcctgtcctctccttgtccgtgccctgtaatttgtgattaacaggaaaactatccggaatgatggatacgttgagacactctgaatcttatcctgtatcttatgatcatgttcatgaagtag

Basic information

species Oryza sativa
transcript 13113.m00214
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00214 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G042253_T01 (Zea mays), 5'ss of exon 2
GCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcgtgctcctgtcctctccttgtccgtgccctgtaatttgtgattaacaggaaaactatccggaatgatggatacgttgagac--actctgaatcttatcctgtatcttatgatcatgttcatgaagtag
||||||| |||||||||| || ||||| || ||| |||| || |||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||||||       || || |  | |  || ||  | | |||  |   | ||  ||       |  ||  | | |  | |||   | ||  |  | || | ||| |    ||  |||||| ||  | ||||| ||||||
GCTGGTCCGACAGGCTGGAGCAAGGACCAATGATATTGCAGGAGATGGTTGTACCACATCCATAATCCTTGCCCAAGGCCTCATTGCTGAAGGGATGAAGgtgtgcctatctcttctctaat-tagttttctatacactggtaacagcgaaaaaagttgctatgat--gaagttgttgatttatagattctgagtcaggatcctgcattgcttcttataattgt-ttcataaagtag
















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|58607174|gb|CK035207.1|CK035207
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|29668864|gb|CB665139.1|CB665139
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58696091|gb|CK084778.1|CK084778
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58693133|gb|CK081820.1|CK081820
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58695701|gb|CK084388.1|CK084388
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|29668478|gb|CB664753.1|CB664753
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58612235|gb|CK039947.1|CK039947
EST:     GTACCACTTCCATAATCCTTGCTCAAGGGCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58694741|gb|CK083428.1|CK083428
EST:     GTACCACTTCCATAATCCTTGCTCAAGGGCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58607710|gb|CK035743.1|CK035743
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|29633815|gb|CB638824.1|CB638824
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAAGAATGAAA                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAA
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58612432|gb|CK040144.1|CK040144
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|29625035|gb|CB630046.1|CB630046
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGTTGAAGGAATGAAG                         GTGCTTGCACCTGGAATTAATCCTGTCCAAATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|29665658|gb|CB661933.1|CB661933
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|29644239|gb|CB649246.1|CB649246
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         T
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtag-
EST: gi|29644239|gb|CB649246.1|CB649246
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         T
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtag-
EST: gi|29644239|gb|CB649246.1|CB649246
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         T
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtag-
EST: gi|58688240|gb|CK076927.1|CK076927
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58689779|gb|CK078466.1|CK078466
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58692874|gb|CK081561.1|CK081561
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58695949|gb|CK084636.1|CK084636
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58605670|gb|CK033703.1|CK033703
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         GTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAG
EST: gi|58691857|gb|CK080544.1|CK080544
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         T
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtag-
EST: gi|58691857|gb|CK080544.1|CK080544
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         T
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtag-
EST: gi|58691857|gb|CK080544.1|CK080544
EST:     GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAG                         T
genomic: GTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtag-

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 45 (downstream exon)
Score: 5

GCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcg ... catgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAGACTGCTTCTGCTTTGGTGTCTGAACTCAGATTGATGTCCCGGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCATAATCCTTGCTCAAGGCCTCATCGCTGAAGGAATGAAGgtgtgttgcgtgctcctgtcctctccttgtccgtgccctgtaatttgtgattaacaggaaaactatccggaatgatggatacgttgagacactctgaatcttatcctgtatcttatgatcatgttcatgaagtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA