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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctagttacatgtacggtcttgatttagaaagttagatatctgtatactgttttatagcttgccgttctcacattcgaaatgcaatgttcatattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCAAACGGTGCTCTGCCAGCCCACAGGAGGGAAGGCCAGGCTCACCGAGGGC

Basic information

species Oryza sativa
transcript LOC_Os02g27769.1
intron # 3
splice site 3'
intron type U2

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|66926521|gb|CX113369.1|CX113369
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88239061|gb|CI240223.1|CI240223
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|86419763|gb|CI054564.1|CI054564
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|89169784|gb|CI110143.1|CI110143
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|86418988|gb|CI053789.1|CI053789
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88283575|gb|CI405021.1|CI405021
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88237988|gb|CI237837.1|CI237837
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88979768|gb|CI026075.1|CI026075
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88214926|gb|CI212964.1|CI212964
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88988287|gb|CI037605.1|CI037605
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|33654259|gb|CF276873.1|CF276873
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88238780|gb|CI238629.1|CI238629
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|86256782|gb|CI061545.1|CI061545
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCTA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88963548|gb|CI029344.1|CI029344
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88992044|gb|CI035182.1|CI035182
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|86251449|gb|CI055582.1|CI055582
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88996308|gb|CI037599.1|CI037599
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCC
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88478898|gb|CI416169.1|CI416169
EST:     ATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTTTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: ATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|86420719|gb|CI056708.1|CI056708
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCC
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|88241823|gb|CI241672.1|CI241672
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|86903165|gb|CI324635.1|CI324635
EST:     AAGTGGCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: AAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
EST: gi|12622591|gb|AU172804.1|AU172804
EST:     GATGTCAAGTGCCAGGGATGCTTCAACAT                         AACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA
genomic: GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCA

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: 29 (upstream exon), 75 (downstream exon)
Score: 121

GATGTCAAGTGCCAGGGATGCTTCAACATgtaataactt ... catattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCAAACGGTGCTCTGCCAGCCCACAGGAGGGAAGGCCAGGCTCACCGAGGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactgttttatagcttgccgttctcacattcgaaatgcaatgttcatattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCAAACGGTGCTCTGCCAGCCCACAGGAGGGAAGGCCAGGCTCACCGAGGGC
                     ttctcac  putative branch site (score: 121)
      ttttata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctagttacatgtacggtcttgatttagaaagttagatatctgtatactgttttatagcttgccgttctcacattcgaaatgcaatgttcatattgcagAACAACCGTGTTCAGCCACTCCCAGACTGTTGTTGTGTGCCCAGGCTGCCAAACGGTGCTCTGCCAGCCCACAGGAGGGAAGGCCAGGCTCACCGAGGGC

- - - - -catgtac
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