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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAGAGGTTTGGGATTCTCTTGGCCGCTGCCCTGCTGGAAGGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagcttatcctagttgttttaaacaatggtctattgctatacagcgacgcaatgattcattgatcatgattggtcgatttagaagtaacttgga...

Basic information

species Oryza sativa
transcript LOC_Os02g03280.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03280.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G027726_T01 (Zea mays), 5'ss of exon 3
AGGAAGAGGTTTGGGATTCTCTTGGCCGCTGCCCTGCTGGAAGGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaa--atgagcttatcctagtt-gttttaaacaatggtctattgctatacagcgacgcaatgattcattgatcatgattggtcgatttagaagtaacttgga-
||||||||||  ||| | ||  |||| |||||||| ||||||||||| || ||||| || || |||||||| || || || |||||| ||||||||  | ||    | ||||  | |      | |   |||| ||     | |  |    ||| |   ||  | ||      |     | |    |||  || | 
AGGAAGAGGTACGGGCTGCTGATGGCGGCTGCCCTCCTGGAAGGGGCGTCGGTTGGACCCCTCATCAAGCTCGCCGTGGAATTTGACCCAAGgtaacgacgaaacgaacctacctagcaccgtatacctgtctctt--cggaaactgttttaatcaa--atcaaacactgcgagctcgatcacgcataagctgtac
















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|5667507|gb|AU077476.1|AU077476
EST:     GCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAAACTGCCATTGCATTTGGGTGCTTCA
genomic: GCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGG-AACTGCCATTGCATTTGGGTGCTTCA
EST: gi|33687051|gb|CF315290.1|CF315290
EST:     GATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAATAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|10794572|gb|AU108538.1|AU108538
EST:     GCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAA-TGCCATTGCATTTGGGTGCTTCAC
genomic: GCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|218479132|gb|FG965046.1|FG965046
EST:     GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|33690587|gb|CF318826.1|CF318826
EST:     GATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|2800946|gb|AA754240.1|AA754240
EST:     GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|10611320|gb|AU108236.1|AU108236
EST:     GGCCTTCTGATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GGCC-TCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|38476716|gb|CF960849.1|CF960849
EST:     GGGGCTTCAGTTGGGCCTCTGATCAAGCTGGCGGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|163925765|gb|EG714601.1|EG714601
EST:     GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|8527280|gb|AU092095.1|AU092095
EST:     TTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGNAACTGCCATTGCATTTGGGTGCTTCAC
genomic: TTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
EST: gi|86847748|gb|CI288816.1|CI288816
EST:     GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAA
genomic: GGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAA
EST: gi|3760266|gb|C97522.1|C97522
EST:     GGGCTTNCAGTT-GGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAG                         CATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC
genomic: GGGCTT-CAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCAC

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: 74 (upstream exon), 64 (downstream exon)
Score: 82

AGGAAGAGGTTTGGGATTCTCTTGGCCGCTGCCCTGCTGGAAGGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagc ... gtgttaccagCATTCTCGTAACAGCATTTGTTGGAACTGCCATTGCATTTGGGTGCTTCACTTGCGCTGCCATCGTTGCCAAGCGTAGGGAGTACCTCTACCTTGGTGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAGAGGTTTGGGATTCTCTTGGCCGCTGCCCTGCTGGAAGGGGCTTCAGTTGGGCCTCTGATCAAGCTTGCTGTAGACTTTGACTCAAGgtaaatgagcttatcctagttgttttaaacaatggtctattgctatacagcgacgcaatgattcattgatcatgattggtcgatttagaagtaacttgga

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