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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttgatctgttcagtgtgtttcgttgtttttctttcaccaaatcaatccttttaacatttttttaaaaatcttaatcatatgccgttctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCCCAGCCCCCAGTGAAGAACGAAGGCCGCGAGGAGGAAGGCGGCCCGGACGACGAGGAAG

Basic information

species Oryza sativa
transcript LOC_Os07g41740.1
intron # 4
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|66916026|gb|CX102874.1|CX102874
EST:     CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACG                         AAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCANGCCC-AGCC
genomic: CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCA-GCCCCAGCC
EST: gi|58593299|gb|CF991607.1|CF991607
EST:     GAGTTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACG                         AAGTCTTCTGAGCCTCGGGCG
genomic: GAGT-GCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCG
EST: gi|58681410|gb|CK070097.1|CK070097
EST:     CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACG                         AAGTCTTCTGAGCCTCGGGCG
genomic: CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCG
EST: gi|58653321|gb|CK042001.1|CK042001
EST:     CGAGTGCTAATAACCACAGCAATAGTAGATCAAAATCCAGCAATTAAACG                         AAGTCTTCTGAGCCTCGGGCGA
genomic: CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCGA
EST: gi|58657324|gb|CK046004.1|CK046004
EST:     CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACG                         AAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCCCAGACCCCA
genomic: CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCCCAGCCCCCA
EST: gi|58682916|gb|CK071603.1|CK071603
EST:     CGAGTGCTAATAACCACAGCAATAGTAAATCAGAATCCAGCAATAAAACG                         AAGTCTTCTGAGCCTCGGGCGAAGCAGGCAAAGCCGCAG
genomic: CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAG
EST: gi|58683778|gb|CK072465.1|CK072465
EST:     CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACG                         AAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCC
genomic: CGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCC

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: 67 (upstream exon), 38 (downstream exon)
Score: 13

TCTTCCCACGATTTTTGAAGTTGTTAGTGGGAAGAGTAAAGCCAAGCCACCGAGTGCTAATAACCACAGCAATAGTAAATCAAAATCCAGCAATAAAACGgtacggccca ... ctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCCCAGCCCCCAGTGAAGAACGAAGGCCGCGAGGAGGAAGGCGGCCCGGACGACGAGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatccttttaacatttttttaaaaatcttaatcatatgccgttctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCCCAGCCCCCAGTGAAGAACGAAGGCCGCGAGGAGGAAGGCGGCCCGGACGACGAGGAAG
                                        ccgttct  CT-rich tract
       ttttaacattttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttgatctgttcagtgtgtttcgttgtttttctttcaccaaatcaatccttttaacatttttttaaaaatcttaatcatatgccgttctgaaagcagAAGTCTTCTGAGCCTCGGGCGAAGCAGCCAAAGCCGCAGCCCCAGCCCCCAGTGAAGAACGAAGGCCGCGAGGAGGAAGGCGGCCCGGACGACGAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
-ttgttga
- - - - - - - - -tgtgttt
- - - - - - - - - - - - -gttgttt
- - - - - - - - - - - - - - - - - - - caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgc