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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttctatgcctcttttgctcttctggaactgtttcctaagattgagctgagcattcaacgtgattttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTTGGGGCACTCGCAAAGTAATCGGTGCTGTTGCCCATGACCTTGGGGCCCA

Basic information

species Oryza sativa
transcript LOC_Os07g26210.2
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|88345678|gb|CI630946.1|CI630946
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|29671833|gb|CB668108.1|CB668108
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|88345748|gb|CI631016.1|CI631016
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|88386860|gb|CI629187.1|CI629187
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|88385299|gb|CI630400.1|CI630400
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|88345785|gb|CI631053.1|CI631053
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|88345885|gb|CI632358.1|CI632358
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAACAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|88348746|gb|CI631440.1|CI631440
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTCCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
EST: gi|88353472|gb|CI631657.1|CI631657
EST:     AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGAT                         CTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT
genomic: AGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTT

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: 75 (upstream exon), 62 (downstream exon)
Score: 18

ACTCATTGGTTTTAGCCCACATATAATTGATGACAGGGAAAATGTAGGGAAGTTTTTATACCTGGAAGGAATAGAGTACTTCATGTGGTGCACTTATGATgtacacttct ... tttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTTGGGGCACTCGCAAAGTAATCGGTGCTGTTGCCCATGACCTTGGGGCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctggaactgtttcctaagattgagctgagcattcaacgtgattttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTTGGGGCACTCGCAAAGTAATCGGTGCTGTTGCCCATGACCTTGGGGCCCA
                                            ttttgct  CT-rich tract
                 taagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacttctatgcctcttttgctcttctggaactgtttcctaagattgagctgagcattcaacgtgattttgctacagCTGTTCTGCGCGAAGATAAAAGTAGAGTCAGGTTTCTTGCTGATGGTACTTGGGGCACTCGCAAAGTAATCGGTGCTGTTGCCCATGACCTTGGGGCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT