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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgttggcccccacatgatccattcccgtctcgatgttatattttgcgtggcaaagacagcgattccgtgggatctgggtttggtactcccaaa...

Basic information

species Oryza sativa
transcript LOC_Os04g51630.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G344279_T01 (Zea mays), 5'ss of exon 2
GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgttggcccccacatgatccattcccgtctcgatgttatattttgcgtggc--aaagacagcgattccgtgggatctgggtttggtactcccaaa-
||  |||||||||||  | | | |||||||||||||||||||||||||||||||||||||| |||| || ||||||||||||||||| || || |||||||||||||||  |  ||  || ||        |  |      |   |  || |   |    |    ||||  | |  |   |||    ||  |  ||    || 
GAAGAAGGAGAAGGCTCTGGTCAAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCACCCGTGCAAAGCAGTACGCCGAGGAATATGATGCCCAGgttagatcgccgctcctaacctgcctgtagactattcgtgcggggtggttggtaggatttatgtgcagcattccattttcatcc---ttatggcctgtggaat

upper sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 2
GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgttggcccccacatgatccattcccgtctcgatgttatattttgcgtggcaaag-acagcgattc-cgtgggatctgggtttggtactcccaaa
||  ||||||||| || | ||||||| ||||||||||||||||| ||| |||||||||||| ||||||||||||||||||||||||||||||| |||||||| |||||    |  ||  |  |||| |  | |   |  |   ||| |  |||| ||        || | ||| |||| |   ||   ||   |   | || 
GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctcctgatcctgctcgatctaacctc-cttgtagactat-tcgtgcggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag

upper sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G094051_T06 (Zea mays), 5'ss of exon 2
GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgttggcccccacatgatccattcccgtctcgatgttatattttgcgtggcaaagacagcgattccgtgggatctgggtttggtactcccaaa---------
||  |||||||||||| | | |||||||||||||||||||||||||||||||||||||||| ||||||| ||||||||||||||||| ||||| |||||||| ||||||  |  ||  || ||         | | | ||   |   |   | ||||     |  ||   |  | || ||   | |||  | |||              
GAAGAAGGAGAAGGCCCTAGTCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCACCCGCGCAAAGCAGTACGCCGAGGAATACGATGCCCAGgtcagatcgccgctcctaacctg---------cctgtagactattcgtgcggggtggttggtagggcttatgtgcggcatgccgttttcatcctcatggcctgtggaat

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|38470057|gb|CF954188.1|CF954188
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|23380534|gb|BU666979.1|BU666979
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|55411844|gb|CV724220.1|CV724220
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|38483035|gb|CF966837.1|CF966837
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|33683621|gb|CF311860.1|CF311860
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58686835|gb|CK075522.1|CK075522
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|88310572|gb|CI659362.1|CI659362
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|218489137|gb|FG964941.1|FG964941
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|29615310|gb|CB620322.1|CB620322
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|29618049|gb|CB623061.1|CB623061
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58599035|gb|CK009563.1|CK009563
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|7378457|gb|AU088728.1|AU088728
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|29687687|gb|CB683962.1|CB683962
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58596632|gb|CK007160.1|CK007160
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|29687177|gb|CB683452.1|CB683452
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58687026|gb|CK075713.1|CK075713
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|5004133|gb|AU069282.1|AU069282
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|218499248|gb|FG947277.1|FG947277
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|5003988|gb|AU069137.1|AU069137
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58602552|gb|CK013080.1|CK013080
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|218489781|gb|FG969217.1|FG969217
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|29618047|gb|CB623059.1|CB623059
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|218490697|gb|FG945225.1|FG945225
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|38475830|gb|CF959963.1|CF959963
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGGGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58589167|gb|CF987475.1|CF987475
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58693620|gb|CK082307.1|CK082307
EST:     TGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGTGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTT
genomic: -GCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAG-GAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTT
EST: gi|33679130|gb|CF307369.1|CF307369
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|218485188|gb|FG948603.1|FG948603
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
EST: gi|58600013|gb|CK010541.1|CK010541
EST:     AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAG                         GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC
genomic: AGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTC

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), 74 (downstream exon)
Score: 75

GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgt ... tgatgagcagGAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgttggcccccacatgatccattcccgtctcgatgttatattttgcgtggcaaagacagcgattccgtgggatctgggtttggtactcccaaa

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccgtctc