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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACGATTTTTTGGTGTCCTCATTGAACACTATGCTGGTGATTTTCCACTTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttcatttactttgatcatctagatgcatgactacatgtgctattaaattaaaagcacccaacttcagttcgtaacagcatcatttatctgaaca...

Basic information

species Oryza sativa
transcript LOC_Os02g33500.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G37550.1 (Glycine max), 5'ss of exon 7
GGAACGATTTTTTGGTGTCCTCATTGAACACTATGCTGGTGATTTTCCACTTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgt------ttgcttcatttactttgatcatctagatgca-tgactacatgtgcta-ttaaattaaaagcacccaacttcagttc-gtaacagcatcatttatctgaaca
|||| |||| |||||  | |||||||| || |||||||||||||||||| | |||||| | ||||| ||||||||  || ||||||| || ||     ||||       | ||       ||||| | || |  ||    ||| || ||||  || ||   |       | | |     | |   || | | ||| ||           
GGAAAGATTCTTTGGCATTCTCATTGAGCATTATGCTGGTGATTTTCCATTATGGCTTTCTCCAATACAAGCTCGAGTTTTACCTGTTACTGATGCCCAGgtaattgactactaagaaatctttggtgatttgtatattctgattatatgttgtacttccctctgctatatctataagaaataaagtgaaaacatgatgc---------

upper sequence: LOC_Os02g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv12s0057g00400.t01 (Vitis vinifera), 5'ss of exon 8
GGAACGATTTTTTGGTGTCCTCATTGAACACTATGCTGGTGATTTTCCACTTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttcatttactttgatcatctagatgcatgactacatgtgctatt----aaattaaaagcacccaacttcagttcg--taacagcatc-atttatctgaaca-
||| ||||| ||||| || ||||| || || |||||||| ||||||||||| |||||| | ||||||||||||||  || |||| ||||| ||||   |||| | ||    ||   ||| |  | || |    |   | ||     | |      || |    ||    | |||   || |  |||||   || || | | |  ||| 
GGAGCGATTCTTTGGAGTTCTCATAGAGCATTATGCTGGGGATTTTCCACTATGGCTTTCTCCAATCCAAGCTCGGGTTTTACCAGTGACGGACACACAGgtattctcagcttctattgtttttttacaaatttagtttcagacattttcctgagaacttgtggctataatctttgctttgagtaacaaattccatgtgtttacacag
















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|25806536|gb|CA762497.1|CA762497
EST:     TTTGGCTTGCCCCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|88974462|gb|CI022003.1|CI022003
EST:     TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|86414324|gb|CI068727.1|CI068727
EST:     TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|66926591|gb|CX113439.1|CX113439
EST:     TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCCAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|88989953|gb|CI018830.1|CI018830
EST:     TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|88225871|gb|CI225787.1|CI225787
EST:     CTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCTAAAGGCATTCGA
genomic: CTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|33381931|gb|CF197274.1|CF197274
EST:     TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|29624983|gb|CB629994.1|CB629994
EST:     TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
EST: gi|38470874|gb|CF955005.1|CF955005
EST:     TTTGGCTAGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAG                         CTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA
genomic: TTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGA

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: 47 (upstream exon), 68 (downstream exon)
Score: 4

GGAACGATTTTTTGGTGTCCTCATTGAACACTATGCTGGTGATTTTCCACTTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttca ... acatttgcagCTGCAATACTGTAACGAGGTGGCTTCAGAACTGAAATCAAAAGGCATTCGAGCTGAGGTATGTCATGGCGAGCGTCTACCAAAGCTAATACGGAATGCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACGATTTTTTGGTGTCCTCATTGAACACTATGCTGGTGATTTTCCACTTTGGCTTGCACCAATCCAAGCTCGTATTCTACCTGTGACAGACAATGAGgtttgcttcatttactttgatcatctagatgcatgactacatgtgctattaaattaaaagcacccaacttcagttcgtaacagcatcatttatctgaaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT