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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAGCTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccggtgttctcctttagtcttccactgttcactctcggttaaagattcttgccaaagctatcccaagttcccaacagctgggagatgatgcagagatccaaatcttttgttttctcttgaatgatgtaatgatgtttttgttccgtggattgttcag

Basic information

species Oryza sativa
transcript LOC_Os11g11050.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g11050.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G139533_T01 (Zea mays), 5'ss of exon 2
AGGAAGCTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccggtgttctcctttagtcttccactgttcactctcggttaa-agattcttgccaaagctatcccaagttcccaacagctgggagatgatgcagagatccaaatcttttgttttctcttgaatgatgtaatgatgtttttgttccgtggattgttcag
|||||||| || |||||| |||| ||||||||||||||| | |||| |||||| |||||||     |  |    |||     |||  || |||   || |  |   |       |   | ||    |       || ||    | | |     |  | |                                                              
AGGAAGCTGCCGCTCGAGATGGAGTACATCGACGTCAAGAGTTCCGCCGATGGCTGgtgagacggagattctctcttctcgattcatctcttcgtccttgactgtcatgcgtgcgtggaggcggagct---cctcctacgatagcgtgccagcgtgggg--------------------------------------------------------------
















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|88581653|gb|CI698853.1|CI698853
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|88388179|gb|CI627718.1|CI627718
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|88730151|gb|CI753766.1|CI753766
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|88579065|gb|CI688033.1|CI688033
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|33680908|gb|CF309147.1|CF309147
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|88317043|gb|CI625680.1|CI625680
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|2427651|gb|C72114.1|C72114
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|88742883|gb|CI766391.1|CI766391
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|88346929|gb|CI628599.1|CI628599
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
EST: gi|88720752|gb|CI744051.1|CI744051
EST:     CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATG                         GAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC
genomic: CTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGC

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: 56 (upstream exon), 64 (downstream exon)
Score: 20

AGGAAGCTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccg ... gattgttcagGAACGCAATCAGAGACATGGTTGTCCGTGGCGCTCCTGCGATTGCCATAGCAGCGGCTTTGGCTCTGGCTGTAGAGGTTTCTGGGTTGGAGGATTTCACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAGCTCCCACTCGAGGTGGACTACATCGACGTCAAGTGCTCCGGCGATGGATGgtgagctccggtgttctcctttagtcttccactgttcactctcggttaaagattcttgccaaagctatcccaagttcccaacagctgggagatgatgcagagatccaaatcttttgttttctcttgaatgatgtaatgatgtttttgttccgtggattgttcag

- - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - GATGGA