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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGATGCTCGGACATTAAATGAGTATCTCAGTACCATGGACCCTTCAACAGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactaggtcacaccttctacagtaagttatatttctgccgggcatgttaatctgaattatttgtttcacttgtgcttttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g50340.1
intron # 2
splice site 5'
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|27548938|gb|CA766971.2|CA766971
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGATGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|86825274|gb|CI359954.1|CI359954
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|88447148|gb|CI531391.1|CI531391
EST:     CAAGATTGGTTGCNGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: CAAGATTGGTTGC-GGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|88544480|gb|CI472582.1|CI472582
EST:     AGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|87039079|gb|CI193701.1|CI193701
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGTTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|86436890|gb|CI118612.1|CI118612
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|86873466|gb|CI329844.1|CI329844
EST:     AGTGCAGGGATT-GTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|3760511|gb|C97765.1|C97765
EST:     CGGGAAGATACAGAAN                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACNTGGTGATGAAC
genomic: CGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|86845050|gb|CI341013.1|CI341013
EST:     GCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: GCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|86889733|gb|CI299931.1|CI299931
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|88465269|gb|CI517438.1|CI517438
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|29628885|gb|CB633896.1|CB633896
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGATGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|89174073|gb|CI041966.1|CI041966
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|86822254|gb|CI357869.1|CI357869
EST:     AGTGCAGGGATT-GTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAA                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
EST: gi|86251728|gb|CI018920.1|CI018920
EST:     AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAG                         TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC
genomic: AGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAAC

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: 45 (upstream exon), 68 (downstream exon)
Score: 6

AGTGATGCTCGGACATTAAATGAGTATCTCAGTACCATGGACCCTTCAACAGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactag ... gcttttgcagTTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGATGCTCGGACATTAAATGAGTATCTCAGTACCATGGACCCTTCAACAGTGCAGGGATTGGTATGTGCGCAAGATTGGTTGCGGGAAGATACAGAAGgtaccactaggtcacaccttctacagtaagttatatttctgccgggcatgttaatctgaattatttgtttcacttgtgcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA