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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccccactatgattttcaacacaaataaatgcaatcttcttataatcagatgcagattctgttttgaaagtgctaattatgggtaaatttccttcag

Basic information

species Oryza sativa
transcript LOC_Os10g37520.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37520.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G067638_T01 (Zea mays), 5'ss of exon 7
CCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccccactatgattttcaacacaaataaatgcaatcttcttataatcagat-----gcagattctgttttgaaagtgctaattatgggtaaatttccttcag----------------------------------------------------------------
|| || ||||||||||| ||||||||  | ||||||||| ||||||||||| |||||||||||||  | |||| |||||||||||| |||||||| |||||||||||  |     |       || ||   |||| || || ||   |  |||  ||     | |    ||  |||| || |   |||         | |||     |                                                                
CCAATAACTGTCATGTTCGGCATGTGCTCCATTTTCCTTCTCATGGCAGCAGTCTTGCAGAGGCGCTTAATGGCTGTCTCTGATCTTCACAGATCGACAAgtatgttaacattgctctacgctaataccg-taaaggccatttttccaccatcgaatcttatgtaagggctagtttggaaatttaaatccccaccggaattctcggggatttaaatttctaaactagccctgaatctgtttggtttctaaccatgacaattttctcctgcag

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 5'ss of exon 7
---------CCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAA-CAAgtatgttccc--cactatgatttt--caacacaaataaatgcaatcttcttataatcagatgcagattctgttttgaaagtgcta-attatgggtaaatttccttcag
         ||||||||||||||||||||||||||  | |||||||| ||  ||||| | |||||||| |||||||| |||||  |  |||      |||  ||||  ||||||  |||   |||  | || ||  | |   ||  |  |  || |||   ||      | ||  | |||  |||||   |  || || |    |             
AATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTG------ACAAGTCAAgtaagtataatccttgcaccgtaatcttgcctatgtaacgagctttaaacttagcatgcaagcaagcccagtctcatttgagccttatacatgacatatg------------
















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|88839829|gb|CI017594.1|CI017594
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAAC--                         AA-CTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|58691691|gb|CK080378.1|CK080378
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86594290|gb|CI251162.1|CI251162
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88969749|gb|CI383252.1|CI383252
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86833582|gb|CI337156.1|CI337156
EST:     TGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: TGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88202560|gb|CI200915.1|CI200915
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|58657621|gb|CK046301.1|CK046301
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86873946|gb|CI334478.1|CI334478
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86845254|gb|CI340363.1|CI340363
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88251581|gb|CI350009.1|CI350009
EST:     TCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: TCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86845514|gb|CI346877.1|CI346877
EST:     GAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: GAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88907822|gb|CI091220.1|CI091220
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86502603|gb|CI145236.1|CI145236
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86837876|gb|CI343263.1|CI343263
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88274829|gb|CI388287.1|CI388287
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|89173922|gb|CI041815.1|CI041815
EST:     TATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86600776|gb|CI356533.1|CI356533
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|7134671|gb|AU082614.1|AU082614
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86492295|gb|CI134928.1|CI134928
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86598275|gb|CI354892.1|CI354892
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86864448|gb|CI334155.1|CI334155
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|86851666|gb|CI315244.1|CI315244
EST:     AATC-TGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGAGCTGGGGAAGATGAGCCGTTAAACCCATAGAAGACA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGA-CTGGGGAAGATGAGCCGTTAAACCCATAGAAGACA
EST: gi|89196087|gb|CI395505.1|CI395505
EST:     ATCTTGCAGAGGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: ATCTTGCAGA-GGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88227301|gb|CI228414.1|CI228414
EST:     CTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
genomic: CTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88268509|gb|CI378444.1|CI378444
EST:     AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAA                         AAGCTGTAGAGATGACTGGGGAAGATGACCCGTTAAACCCATAGAAGACAA
genomic: AATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA
EST: gi|88850535|gb|CI093216.1|CI093216
EST:     AGAGGCGGCTGATGGTTGTCTCTGATCTCCTCAGATCAACCA                         AAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGTAGACTA
genomic: AGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAA

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: 50 (upstream exon), 73 (downstream exon)
Score: 24

CCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccc ... tttccttcagAAGCTGTAGAGATGACTGGGGAAGATGAGCCGTTAAACCCATAGAAGACAAGACAATAGATGTGAATTGGACATGAAAATTGCCATCCAACTTGAGCCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCCACAGATCAACAAgtatgttccccactatgattttcaacacaaataaatgcaatcttcttataatcagatgcagattctgttttgaaagtgctaattatgggtaaatttccttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA