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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattccatatctttgttaataatatgaaaagtaacttgaaacatttcgattcccacatgaatcctagaaacttccaacatttaaaataaaacctg...

Basic information

species Oryza sativa
transcript LOC_Os01g68710.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68710.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G153991_T01 (Zea mays), 5'ss of exon 3
TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattccatatctttgttaataatatgaaaagtaacttgaaacatttcgattcccacatgaatcctagaaacttccaacatttaaaataaaacctg--
|||||||| |||||||| || |||||||| ||||||||||||||||| || || || |||||||||||||    || | | || |  |             | ||   |||||  || |      |   ||   ||     ||         | |    | ||  
TACAAGCCTGAGTCATGTACGCTGCAAGCACACAAAGGAGACAAAATTAAGGTTCACTATCGTgtaagtacctgatctgtatgcttttttagccttgctctattttccacatt--gactttttttttgttcagtgatgtagccctgtaagggatttgctcatggg

upper sequence: LOC_Os01g68710.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G031204_T01 (Zea mays), 5'ss of exon 3
TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattccatatctttgttaataatatgaaaagtaacttgaaa---catttcgattcccacatgaatcctagaaacttccaacatttaaaataaaacctg
||||| || |||||||| ||||||||||| |||||||||||||| || || || |||||||||||||| ||   ||  || | | |||  | |  |   |  ||  |     ||  | ||||     |   ||  |||     |     ||||          || 
TACAAACCGGAGTCATGTACCCTGCAAGCACACAAAGGAGACAAGATTAAGGTTCATTATCGTgtaagcatctgat--ctgtataaattttttttagctttgctgcattttccacattgatttttttagtgatg-tagtccggtaagggatttgctcatggtgcta
















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|88723075|gb|CI746585.1|CI746585
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55436956|gb|CV731667.1|CV731667
EST:     TCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: TCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55440369|gb|CV733494.1|CV733494
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88723491|gb|CI747001.1|CI747001
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55409944|gb|CV722320.1|CV722320
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55438455|gb|CV732524.1|CV732524
EST:     AAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: AAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88723609|gb|CI747119.1|CI747119
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88722134|gb|CI745461.1|CI745461
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|568861|gb|D39710.1|D39710
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|33659572|gb|CF282185.1|CF282185
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|8527930|gb|AU092745.1|AU092745
EST:     CATGCACCNTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|163923518|gb|EG711137.1|EG711137
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88344739|gb|CI624390.1|CI624390
EST:     CATGCACCCTGCAAGCTCACAAAGGAGAAAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88723542|gb|CI747052.1|CI747052
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|86829242|gb|CI284927.1|CI284927
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55436954|gb|CV731666.1|CV731666
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|58589883|gb|CF988191.1|CF988191
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACA
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACA
EST: gi|11171677|gb|AU163906.1|AU163906
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55433322|gb|CV729734.1|CV729734
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88726773|gb|CI750428.1|CI750428
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55413431|gb|CV725807.1|CV725807
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|2442348|gb|C74119.1|C74119
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55433324|gb|CV729735.1|CV729735
EST:     AAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: AAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55414253|gb|CV726629.1|CV726629
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55412950|gb|CV725326.1|CV725326
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88827090|gb|CI777655.1|CI777655
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|9055415|gb|AU097613.1|AU097613
EST:     AAATCCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: AAAT-CAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|2442460|gb|C74231.1|C74231
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGA
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACT-GATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGA
EST: gi|86829393|gb|CI285036.1|CI285036
EST:     TCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: TCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|27547036|gb|CA765286.2|CA765286
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCANGTGTTTGATTCTAGCTATGACAGAGGTGA
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCA-GTGTTTGATTCTAGCTATGACAGAGGTGA
EST: gi|55441436|gb|CV734038.1|CV734038
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88207641|gb|CI207490.1|CI207490
EST:     TGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: TGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|33685240|gb|CF313479.1|CF313479
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|55413109|gb|CV725485.1|CV725485
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|51946051|gb|CV152392.1|CV152392
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|163928575|gb|EG711160.1|EG711160
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGTATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|88242499|gb|CI242348.1|CI242348
EST:     AAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: AAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|428562|gb|D24714.1|D24714
EST:     CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGT                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: CATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC

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), 63 (downstream exon)
Score: 45

TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattc ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGACCCCTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAAGCCAGAGTCATGCACCCTGCAAGCTCACAAAGGAGACAAAATCAAAGTGCATTATCGTgtaagtattccatatctttgttaataatatgaaaagtaacttgaaacatttcgattcccacatgaatcctagaaacttccaacatttaaaataaaacctg

- - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa