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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttgatgactccatggtttctttatttgtgtttttgtttatttaacaagtactgtaataatgcttcaatcaaacaatcag

Basic information

species Oryza sativa
transcript LOC_Os11g03730.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.3 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 14
TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttgatgactccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcag
|||| | ||||||||||||||||| || ||||||||||||||| ||||||| ||||||||||| ||  ||  |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||
TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcag

upper sequence: LOC_Os11g03730.3 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G006130_T01 (Zea mays), 5'ss of exon 15
TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttgatgactccatggt-ttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcag
|||| | ||||||||||||||||| || ||||||||||||||| ||||||| ||||||||||| ||  ||  |   |  |   || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||
TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattcttggtttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcag

upper sequence: LOC_Os11g03730.3 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 16
TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttgatgactccatggtttctttatttgtgtttttgtttatttaacaagtactgtaataatgcttcaatc--aaacaatcag------------
|||||||||| |||||||||| ||||||||||| || |||||   ||||||    ||||  || |       | |     | ||  |    ||  ||  || ||  | | |    |  |  |||  || |||    || |||               
TGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGACgtatgtctcctcattttc----ctactaaaaccttgccttcatt-atacatctatacttaaatcaatatttaaatttggaaaaattttctctcgttaaag

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|29665627|gb|CB661902.1|CB661902
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29636384|gb|CB641393.1|CB641393
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29674665|gb|CB670940.1|CB670940
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29677794|gb|CB674069.1|CB674069
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|87021358|gb|CI295417.1|CI295417
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29627661|gb|CB632672.1|CB632672
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29624426|gb|CB629437.1|CB629437
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|38476158|gb|CF960291.1|CF960291
EST:     CAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: CAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|33795281|gb|CF323512.1|CF323512
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAA
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAA
EST: gi|29646542|gb|CB651549.1|CB651549
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29628284|gb|CB633295.1|CB633295
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|86905528|gb|CI285491.1|CI285491
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29681803|gb|CB678078.1|CB678078
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29624428|gb|CB629439.1|CB629439
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29627934|gb|CB632945.1|CB632945
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|29644766|gb|CB649773.1|CB649773
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|86851229|gb|CI312630.1|CI312630
EST:     ATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATC-AAC                         GTTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTC
genomic: ATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagG-TGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTC
EST: gi|29638132|gb|CB643141.1|CB643141
EST:     GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
EST: gi|86481297|gb|CI123930.1|CI123930
EST:     TTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: TTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC

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: 57 (upstream exon), 74 (downstream exon)
Score: 65

TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCCTAGTTACTGGATGCAGACTCTTTTCGGTGAATCTAGCGGTGCTATGTTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttgatgactccatggtttctttatttgtgtttttgtttatttaacaagtactgtaataatgcttcaatcaaacaatcag

- - - - - CAGATG