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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagaagcaaatgatatggaaacagtgagaattctaatgagatgtactttatttttaggaattttatcttcctctgatggtggcttttttctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCTGTCAAGGCATTCAGCAGTCGCATGCATCTTTCTCTTGGGGCAGGATTAA

Basic information

species Oryza sativa
transcript LOC_Os07g42500.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g42500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G108767_T02 (Zea mays), 3'ss of exon 3
aaagaagcaaatgatatggaaacagtg-agaattctaatgagatgtactttattt-ttaggaattttatcttcctctgatggtggcttttttcttt---ttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCTGTCAAGGCATTCAGCAGTCGCATGCATCTTTCTCTTGGGGCAGGATTAA
        |   ||||| | | || || | |  | | |     |   | | | |  ||||    ||||  | | | |||||||||| ||| | | |   |||||| |||| || ||||||||||| || || ||||| |||||||| ||||| ||||||||||| |||||||||||||| |||||||| |||||||||||||| |
-----gatagtagatattggagcaatgtaaagatgtgagtgcttaagcataagtcattagagtctttaattccatttgatggtggcctttctttgtatattccagATTGGAGGAGAACTGACAGACTTCATCATTGTGCTTCATGACCGTAAAGCTGTCAAGGCTTTCAGCAGTCGCATTCATCTTTCACTTGGGGCAGGATTGA
















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|89182383|gb|CI113752.1|CI113752
EST:     GTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88246304|gb|CI246153.1|CI246153
EST:     GTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTAATAATTGTACTTCATGATCGTAAGCCT
genomic: GTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88270054|gb|CI381352.1|CI381352
EST:     TGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: TGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88516404|gb|CI444058.1|CI444058
EST:     ATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: ATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|89174859|gb|CI111057.1|CI111057
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88262827|gb|CI364405.1|CI364405
EST:     TCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: TCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|58597717|gb|CK008245.1|CK008245
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86895314|gb|CI331236.1|CI331236
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86498113|gb|CI140746.1|CI140746
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86490969|gb|CI133602.1|CI133602
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86541628|gb|CI181834.1|CI181834
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCCGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88989753|gb|CI107440.1|CI107440
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|89184604|gb|CI007029.1|CI007029
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86490986|gb|CI133619.1|CI133619
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88519265|gb|CI446919.1|CI446919
EST:     GCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|29637422|gb|CB642431.1|CB642431
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88404026|gb|CI601436.1|CI601436
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|89190211|gb|CI392261.1|CI392261
EST:     CCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: CCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|8527377|gb|AU092192.1|AU092192
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88278930|gb|CI397734.1|CI397734
EST:     CATCTGTTTGGCCTGGGATGGGGAGTTCACG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGG
genomic: CATCTG-TTGGCCTGGGATGGGGAGTTCA-Ggtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAA-GG
EST: gi|88831341|gb|CI082151.1|CI082151
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86431007|gb|CI083430.1|CI083430
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86595813|gb|CI286715.1|CI286715
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATAGTACTTCATGATCGTAAGG
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGG
EST: gi|29639152|gb|CB644161.1|CB644161
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|86853376|gb|CI327854.1|CI327854
EST:     TGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: TGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
EST: gi|88829557|gb|CI074427.1|CI074427
EST:     GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAG                         TTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT
genomic: GGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCT

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: 70 (upstream exon), 70 (downstream exon)
Score: 21

ATACAAAGTTGGCACTGGCCTTGTAGTTGCCCGAAGATCAGATGGATCATGGTCTGCCCCATCAGCAATTGCATCTGTTGGCCTGGGATGGGGAGTTCAGgtttttgtcc ... ctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCTGTCAAGGCATTCAGCAGTCGCATGCATCTTTCTCTTGGGGCAGGATTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttatttttaggaattttatcttcctctgatggtggcttttttctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCTGTCAAGGCATTCAGCAGTCGCATGCATCTTTCTCTTGGGGCAGGATTAA
                          ctctgat  putative branch site (score: 21)
                                   tggcttttttcttttt  putative PPT
     atttttaggaatttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagaagcaaatgatatggaaacagtgagaattctaatgagatgtactttatttttaggaattttatcttcctctgatggtggcttttttctttttccagTTTGGTGGCGAACTGACAGATTTTATAATTGTACTTCATGATCGTAAGGCTGTCAAGGCATTCAGCAGTCGCATGCATCTTTCTCTTGGGGCAGGATTAA

- - - gcaaatg
- - - - - - - - - gaaacag
- - - - - - - - - - - - - - - - - - - - gatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggc