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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttagatgtgtgcggaactaaagaaaatgttcaggcatttctgtacttgcaaaaatattgctcttctctgtatttgttctaattccatgtttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGAATACACAGCTGACGAAATCCAATCAATTGGTATGTTGCCTATACCCGAC

Basic information

species Oryza sativa
transcript LOC_Os08g34970.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34970.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM5G825854_T02 (Zea mays), 3'ss of exon 24
--acttagatgt---gtgcggaactaaagaaaatgttcaggcatttctgtacttgcaaaaatattgctcttctctgtatttgttctaattccatgtttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGAATACACAGCTGACGAAATCCAATCAATTGGTATGTTGCCTATACCCGAC
  || ||  |||          | || ||| ||   | |   |  | |  ||| |  ||||   | ||       |||||| ||       |   || | | ||||||||||||||||||||||||||||||||| || |||||||||||||| || ||| |   ||| ||||| ||||| || ||||||||||| ||||| |||
ttacctaactgttctacttcagagtacagagaac-cttacctaaatgtaaactggagaaaaaggttctg----aagtatttctttatgcctctctttggccgcagGACAAATATAGTTGAGGCTCATATACAGCTGCATTCCCTTCTGAAGTCGGAGTACTCTAGTGAAGAAATGCAATCCATCGGTATGTTGCCGATACCTGAC
















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|86835816|gb|CI348230.1|CI348230
EST:     TTGTATTTGCAAAATCCATGTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|33687148|gb|CF315387.1|CF315387
EST:     TGTATTTGCAAAATCCATCTACGCGGNTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TGTATTTGCAAAATCCATCTACGCGG-TTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|86436875|gb|CI118597.1|CI118597
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCCATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|87017918|gb|CI273940.1|CI273940
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|25806151|gb|CA762112.1|CA762112
EST:     TTGTATTTGCAAAATCCATTTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACCCTCCCTTTTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|29642984|gb|CB647991.1|CB647991
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|88521654|gb|CI449362.1|CI449362
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|88381965|gb|CI530771.1|CI530771
EST:     TGTATTTCCANAATCCATCTAGCGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGGTACACTCCCTTCTGAAGTCAGA
genomic: TGTATTTGCAAAATCCATCTA-CGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|88291548|gb|CI537334.1|CI537334
EST:     TTGTATTTGCAAAATCCATGTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGGTCATATACAGGTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|88295656|gb|CI530219.1|CI530219
EST:     TTGTATTTGCAAAATCCATGTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGGTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|88260378|gb|CI362671.1|CI362671
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|58657979|gb|CK046659.1|CK046659
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|86853006|gb|CI324708.1|CI324708
EST:     T-TATTTGCAAAATCCATCTAGCGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGGTACACTCCCTTCTGAAGTCAGA
genomic: TGTATTTGCAAAATCCATCTA-CGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|33687147|gb|CF315386.1|CF315386
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|86874604|gb|CI318163.1|CI318163
EST:     AATCCATCTACGCGGTTGATTTGATTCAAACCAATCAA                         GACAAATATAG-TGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: AATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|88455474|gb|CI521694.1|CI521694
EST:     TTGTATTTNCAAAATCCATTTACGCGGTTGATTTTATTCAAACCAATCAA                         GACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
EST: gi|86481593|gb|CI124226.1|CI124226
EST:     TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCGAACCAATCAA                         GACNAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA
genomic: TTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGA

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), 61 (downstream exon)
Score: 20

TTGGGACTGCTATTCAGCAAGATTTACCCAAAGTAATGACCATGATGAGGTTGTATTTGCAAAATCCATCTACGCGGTTGATTTTATTCAAACCAATCAAgtaagtattt ... tttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGAATACACAGCTGACGAAATCCAATCAATTGGTATGTTGCCTATACCCGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgcaaaaatattgctcttctctgtatttgttctaattccatgtttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGAATACACAGCTGACGAAATCCAATCAATTGGTATGTTGCCTATACCCGAC
                                ttctaat  putative branch site (score: 20)
                                             tttgtctc  putative PPT
                          tatttgttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttagatgtgtgcggaactaaagaaaatgttcaggcatttctgtacttgcaaaaatattgctcttctctgtatttgttctaattccatgtttgtctcagGACAAATATAGTTGAGGCTCATATACAGCTACACTCCCTTCTGAAGTCAGAATACACAGCTGACGAAATCCAATCAATTGGTATGTTGCCTATACCCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - -tgtgtgc
- - - - - - - -gaactaa
- - - - - - - - - - - agaaaatg
- - - - - - - - - - - - - - - - caggcat
- - - - - - - - - - - - - - - - - - - - - - -acttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccatg