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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcatacctgtcagcgtcttaatcttgacctgaacattttcatacttcaatggtaatctcaggcgatcgttttttcatcacag

Basic information

species Oryza sativa
transcript LOC_Os01g13190.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G058584_T01 (Zea mays), 5'ss of exon 14
GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcatacctgtcagcgtcttaatcttgacctgaacattttcatacttcaa-----tggtaatctcaggcg-atcgttttttcatcacag----------------------------
|| || |||||||| ||| |||||||||||||||||||||||||||| |||||||||||||| |||||||||||  |  |||| || |||||||  ||||||  | |       |||   |||   ||  ||  ||  | ||||||     ||||   |   || | |||  | ||  ||    |                            
GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgta--ggcatattttttttgtcattagctttggtgtggtcacatt-gttcttcaagcagatggttccccttggggcatcaatcttgaattcttgatcgaaatatttggtttctttacctcag
















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|88907696|gb|CI091094.1|CI091094
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|29685418|gb|CB681693.1|CB681693
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86426596|gb|CI071693.1|CI071693
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86493486|gb|CI136119.1|CI136119
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|88227348|gb|CI226828.1|CI226828
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|58607312|gb|CK035345.1|CK035345
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|29680233|gb|CB676508.1|CB676508
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|33801600|gb|CF326672.1|CF326672
EST:     CTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|88222978|gb|CI222827.1|CI222827
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86502909|gb|CI145542.1|CI145542
EST:     GGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: GGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86257328|gb|CI004146.1|CI004146
EST:     GGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: GGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|29662202|gb|CB658477.1|CB658477
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTTGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|88966139|gb|CI013015.1|CI013015
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|218487285|gb|FG960895.1|FG960895
EST:     CTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86834033|gb|CI340172.1|CI340172
EST:     ATGTAAA-GATGCTGAACAGTGGGA-GATCTTGTCGAGAATGCAG                         GGTC-GTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: ATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86481451|gb|CI124084.1|CI124084
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|88843810|gb|CI011068.1|CI011068
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86488622|gb|CI131255.1|CI131255
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86500662|gb|CI143295.1|CI143295
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACGATGGACCCCGGAGAGCGTGGGCGACTATGCCA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATG-CA
EST: gi|86859953|gb|CI321932.1|CI321932
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTGGTCGAGAATGCAG                         GGTCGGGTCTTCTTGGGACAATGGACCCCGGATAGCGTGGGCGACTATGCA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTC-GGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCA
EST: gi|29685419|gb|CB681694.1|CB681694
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|86831296|gb|CI297565.1|CI297565
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
EST: gi|29663864|gb|CB660139.1|CB660139
EST:     CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG                         GGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA
genomic: CATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAA

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), 71 (downstream exon)
Score: 23

GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcat ... ttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAAGCGGCACAAACCATGTCCTTCCAACCTATGGTTACGCAAGGATGTATAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcatacctgtcagcgtcttaatcttgacctgaacattttcatacttcaatggtaatctcaggcgatcgttttttcatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT