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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttactgtgctatctagttgcaatgatggaactatattttattctgtatatcaagattatctcagctaattttcaatttgcacctttcgtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGCTACAGCAGTTGTCGTGAACAAAAGGAGAAGGAACATGCTTAAAGAGTTG

Basic information

species Oryza sativa
transcript LOC_Os07g12110.1
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|38471465|gb|CF955596.1|CF955596
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|218479043|gb|FG955974.1|FG955974
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|29688863|gb|CB685138.1|CB685138
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|4968729|gb|AU065633.1|AU065633
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|29617589|gb|CB622601.1|CB622601
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|33794207|gb|CF322994.1|CF322994
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|218481869|gb|FG961133.1|FG961133
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|58671192|gb|CK059878.1|CK059878
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|218501745|gb|FG957162.1|FG957162
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|33795947|gb|CF323841.1|CF323841
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTG
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTG
EST: gi|33677618|gb|CF305857.1|CF305857
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|4968805|gb|AU065709.1|AU065709
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|58694550|gb|CK083237.1|CK083237
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|29645460|gb|CB650467.1|CB650467
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|33794202|gb|CF322991.1|CF322991
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|218491612|gb|FG958894.1|FG958894
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCGATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
EST: gi|117243527|gb|CT843109.1|CT843109
EST:     AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAG                         GTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC
genomic: AACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGC

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: 62 (upstream exon), 54 (downstream exon)
Score: 52

AGCTCCAGAATAGGATATGGCTGATGCATTGGAGTATTTTTATCTTCTTTAACCATGAAAACGGCAGAAATGGGATCATCGATCTGTTCTTCCAGGATAGgtttgtttac ... gtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGCTACAGCAGTTGTCGTGAACAAAAGGAGAAGGAACATGCTTAAAGAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtatatcaagattatctcagctaattttcaatttgcacctttcgtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGCTACAGCAGTTGTCGTGAACAAAAGGAGAAGGAACATGCTTAAAGAGTTG
                    agctaat  putative branch site (score: 52)
                                       cctttcgtct  putative PPT
                       taattttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttactgtgctatctagttgcaatgatggaactatattttattctgtatatcaagattatctcagctaattttcaatttgcacctttcgtctaaccagGTACTTGAACGCAATCCAGACAAATGCACCCCATCTTCTGAGATACCTTGCTACAGCAGTTGTCGTGAACAAAAGGAGAAGGAACATGCTTAAAGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - ctgtgct
- - - - - - - - - - tgcaatg
- - - - - - - - - - - - - - - - - - - - - -ttctgta