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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaaacttacaattgatactagatactgttacatgtggtatcatttttcttccatttgatcataaacatggtgcttaattctatgct...

Basic information

species Oryza sativa
transcript LOC_Os03g26970.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G41330.1 (Glycine max), 5'ss of exon 9
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaaacttacaattgatactagatactgttacatgtggtatcatttttcttccatttgatcataa-acatggtgcttaattctatgct
|| ||||||||||| ||||| || || |||||||| || ||||||||||||||||| || ||||||||||| ||||||||||| ||||||||   |   ||| |       |  |  | | ||  |||    ||    |   |||||  |   | ||  ||| |      |||  |  | |      
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcaatagcagttctgcaagcaaaatg-tgtggagtgcatcaattttttttgtgtttgtgtccattatgtgctgtggctggtaccccttg

upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 8
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaaacttacaattgatactagatactgttacatgtgg-tatcatttttcttccatttgatcataaacatggtgcttaattctatgct
|| |||||||| || ||||| || || |||||||| || ||||||||||||||||| || ||||||||||| ||||||||||| ||||||||   |   ||| | |     |  |  | | |   |||   | |||  |   | |||  ||   | |  |    |  ||| ||||     | |  | 
GTGGATCCATCGGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcaatagtagttctgcaagcaaaagcatgtgtgaagtgaatcagaatttgtttttgtgttgtgtccattatg-tgctgtggcccacacc

upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G16660.1 (Glycine max), 5'ss of exon 9
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaaacttacaattgatactagatactgttacatgtggtatcatttttcttccatttgatcataaacatggtgcttaattctatgct----
|| ||||||||||| ||||| || || |||||||| || ||||||||||||||||| || ||||||||||| ||||||||||| ||||||  |||||         |    || || | |  |  | || | |     |  |       | ||| |  || | || |  ||  | |||| | || |    
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagatttgtcgtgtctttt-ttaatgc-atctcttcttcccttaccaaaaaaaaaggatgcatatcttcttcaaaa--gttgtcaattttgtggtttgg

upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G17810.3 (Glycine max), 5'ss of exon 9
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaaacttacaattgatactagatactgttacatgtggtatcatttttcttccatttgatcataaacatggtgcttaattctatgct--
|| ||||||||||| ||||| || || |||||||| || ||||||||||||||||| || ||||||||||| ||||||||||| ||||||||   |   ||  |       || |  | | |   |||    ||    |  |||| |  |   | |   ||| ||  |  || | || ||| |     
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcagtaacagttcttcaagcaaaaacatgtggagtgcatcaaaatttgttgtgt-tgtatccattaa-gtactgatgaaatctgtctgtg

upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaa--acttacaattgatactagata-ctgttaca-----tgtggtatcatttttcttccatttga---tcataaacat-ggtgcttaattctatgct------------------------------------------------------
|| |||||||| || || || |||||||||||||| ||||| |||||||| || || || |||||||| || || |||||||||||||||     || ||||     | | |    |   || ||| |   || |     | ||  |   || || | | | |  |   ||   || || ||  | |      |   |                                                      
GTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAGgtaatactgtttacaatttgttgatatccaaagatatataaccagtatactgattttgaaaattttcttttactactcaaatttcgataatataggctcctgtcataacaatatgaaaccactcttcgtcgctgacaaaccttaaccaattacgatttccttgcag

upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 5'ss of exon 9
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaa--gcagattgacaaaacttacaattgatactagatactgtta-catgtggtatcatttttcttccatttgatcataaacatggtgcttaattctatgct
|| |||||||| || || || ||||| |||||||| || || ||||| || ||||| || ||||||||||| ||||||||||| |||| |    |  ||  ||    |    ||   |    |||  ||  | |||||  | |||| ||  |    ||||||||                         
GTGGATCCATCTGGCTCTTATTTCTCATGGAAAGCTTCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtgataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtcatttcatcttagtc---tttgatcag------------------------

upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 8
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaa-acttacaattgatactagatactgttacatgtggtatc--atttttcttccatttgatcataaacatggtgcttaattctatgct
|| ||||||||||| ||||| ||||| |||||||| || || |||||||| ||||| |||||||||||||||||||||||||| |||||   | ||    |     || |  |   |  |  | |   |  || |  | | |  || ||| ||   |||||| |              | || | |   
GTGGATCCATCAGGTTCATATTTCTCATGGAAAGCCTCCGCAATGGGGAAGAATGTCTCAAATGCAAAGACATTTCTTGAGAAGAGgtatttaaatcagaatttggttgctgtgtctttttaaaatgatatcaagcagcagcctatctttattgtgtttgat-acttttgcaacaacaattttttta--

upper sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaaacttacaattgatactagatactgttacatgtggtatcatttttcttccatttgatcataaacatggtgcttaattctatgct----------------------------------------------
|| ||||||||||| ||||||||||| ||||| |||||||| || || || |||||||| ||||| ||||| ||  | ||||||||||  |    ||  || |  || || |   |  | ||| ||||    |  | | |  |           |   |  | |||  |  | ||  |   ||  |                                              
GTAGATCCATCAGGATCATACTTCTCATGGAAGGCATCAGCAATTGGCAAGAATGTGTCTAATGCGAAGACTTTCTTAGAGAAAAGgtcggtcctttc-catacgttgcactctgttttcgattctgtagtctacgatgtggtagaatgcaggatgagttttgaacgagacgattcgtgtcatatttaatatgagatagtgactcattcgagaggcatactgttacaagcag

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|27548112|gb|CA766216.2|CA766216
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGACATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|33654276|gb|CF276890.1|CF276890
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|55408396|gb|CV720772.1|CV720772
EST:     GTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: GTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88239397|gb|CI240559.1|CI240559
EST:     TTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|58031158|gb|CX728701.1|CX728701
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88238655|gb|CI238504.1|CI238504
EST:     CAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: CAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88238554|gb|CI238403.1|CI238403
EST:     AAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: AAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|89193863|gb|CI018181.1|CI018181
EST:     CAGCTTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: CAGC-TATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|218489822|gb|FG967489.1|FG967489
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGACATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88510139|gb|CI437645.1|CI437645
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88205175|gb|CI205024.1|CI205024
EST:     TGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|66923272|gb|CX110120.1|CX110120
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88199790|gb|CI199640.1|CI199640
EST:     GTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: GTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88252854|gb|CI350279.1|CI350279
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88460463|gb|CI531936.1|CI531936
EST:     TGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|33691029|gb|CF319268.1|CF319268
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88222631|gb|CI222587.1|CI222587
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88215513|gb|CI215362.1|CI215362
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAGAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|88289738|gb|CI525070.1|CI525070
EST:     AAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: AAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|11233514|gb|AU164926.1|AU164926
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|86512001|gb|CI154634.1|CI154634
EST:     GCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: GCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|33808226|gb|CF330002.1|CF330002
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
EST: gi|8859749|gb|AU097067.1|AU097067
EST:     TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG                         ATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC
genomic: TCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAAC

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: 65 (upstream exon), 63 (downstream exon)
Score: 34

GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagat ... ttcattgcagATACACAGAAGATATGGAGCTTGACGATGCCATTCATACTGCTATTTTAACTCTGAAAGAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAGgtaagcagattgacaaaacttacaattgatactagatactgttacatgtggtatcatttttcttccatttgatcataaacatggtgcttaattctatgct

- - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG