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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctctagtgactttattgattggtgagaaaccagagcgttataactttggttatccttatttgtcagccttttgagaggaaatgttgaaacacattctagcttttaaaaagtctgtcttctttgagatgactaaaaaaaatgtctctgatatttcctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGCTCAAAGACACAACAG

Basic information

species Oryza sativa
transcript LOC_Os02g50860.1
intron # 5
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|33809743|gb|CF330761.1|CF330761
EST:     AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAG                         GGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
genomic: AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
EST: gi|163928524|gb|EG711409.1|EG711409
EST:     AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAG                         GGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
genomic: AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
EST: gi|86497574|gb|CI140207.1|CI140207
EST:     AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAG                         GGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
genomic: AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
EST: gi|58679076|gb|CK067763.1|CK067763
EST:     ATCCTGGCATAATACCTGTTACCACAGCACA-                         GGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
genomic: ATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
EST: gi|44676265|gb|CR289699.1|CR289699
EST:     AGCACTACTTGTTGGACCATCCTGCCATGATACCTGTTACCACAGCACAG                         GGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
genomic: AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
EST: gi|33815650|gb|CF333676.1|CF333676
EST:     AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAG                         GGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAG
genomic: AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGG-TGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAG
EST: gi|86495788|gb|CI138421.1|CI138421
EST:     AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAG                         GGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC
genomic: AGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGC

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: 33 (upstream exon), 74 (downstream exon)
Score: 17

ATCTCCGTGAAGACAAGCACTACTTGTTGGACCATCCTGGCATGATACCTGTTACCACAGCACAGgtatatctct ... cctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGCTCAAAGACACAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctgtcttctttgagatgactaaaaaaaatgtctctgatatttcctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGCTCAAAGACACAACAG
                                        tatttcctctt  CT-rich tract
                 atgactaaaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatctctagtgactttattgattggtgagaaaccagagcgttataactttggttatccttatttgtcagccttttgagaggaaatgttgaaacacattctagcttttaaaaagtctgtcttctttgagatgactaaaaaaaatgtctctgatatttcctcttgtagGGTGAAGAACTTCGAAAACAAATAGGTGCTGCTTATTACATTGAGTGCAGCTCAAAGACACAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA