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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaaacaaatgaaaaccctaatttatctgtaatttttttaagtagtggactcaaacataaatattttgaaataacaccgtcaactttcaatttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCTCTTGCTGTCGCCTGCTATGACCTCTCACAGTTCCTTCAGTACCACCCTT

Basic information

species Oryza sativa
transcript LOC_Os07g36470.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g36470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G019999_T01 (Zea mays), 3'ss of exon 8
ttcaaacaaatgaaaaccctaatttatctgtaatttttttaagtagtggactcaaacat--aaatattttgaaataacaccgtcaactttcaatttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCTCTTGCTGTCGCCTGCTATGACCTCTCACAGTTCCTTCAGTACCACCCTT
   |     |||     | |   ||  |||      ||||| |||| |  |  || |||  |  | | | |   | |     |      |  |  || ||||||||| || || || ||||||||||| ||||||||    ||||| || |||||||| || |||||||| ||||||||||| |||||||||||||| || |
-ataccgggatggcggtcttttcttccctggccgagttttaggtag-gctcataagcattcagctctgtggttgtgatgaaattgcacctataacttggcagATTCTGCGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAATTCCTTCAGTACCATCCAT

upper sequence: LOC_Os07g36470.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G163233_T04 (Zea mays), 3'ss of exon 11
---------------------------------------------------------------------------------------ttcaaacaaatgaaaaccctaatttatctg---taatttttttaagtag-tggactca--aacat--aaatattttgaaataacaccgtcaactttcaatttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCTCTTGCTGTCGCCTGCTATGACCTCTCACAGTTCCTTCAGTACCACCCTT
                                                                                       ||       ||  | |  ||| | |         ||| || |  | ||| | | ||||  | |||  |  | | | |   | |     |     ||  |  || |||||||||||| || || ||||||||||| ||||||||    ||||| || |||||||| || |||||||| ||||||||||||||||| |||||||| || |
gtatgccttgccctttcttctttgggacaattgtgattatacccttcgctggtcttgcaattgtgattttaccctccgttttccaactttgtgttcatagataagctattctggacaattcaatgttatagattagataggctcacaagcatttagctctgtggttgtgatgaaattgcacttataacttggcagATTCTACGAGTTCTCATGACAATCATTGACACATCAAGTGACACCACCGCTCTTGCCGTGGCCTGCTACGACCTCTCACAGTTCCTCCAGTACCATCCAT
















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|8858217|gb|AU095535.1|AU095535
EST:     CAAGTTTCTGGCGCGAGNACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|218491215|gb|FG953120.1|FG953120
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|86486918|gb|CI129551.1|CI129551
EST:     AACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATGATCGACACATCGGCCGACACGACTGCT
genomic: AACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|86429795|gb|CI082218.1|CI082218
EST:     AAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: AAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|33804925|gb|CF328340.1|CF328340
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|86522340|gb|CI162546.1|CI162546
EST:     TAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: TAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|88998146|gb|CI038031.1|CI038031
EST:     TGAAGAAAATGATGTCCAG                         ATTGTACGTGTGCTTTATGACAATCATCGACACATCGGCCGACACGACTGC
genomic: TGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGC-TTATGACAATCATCGACACATCGGCCGACACGACTGC
EST: gi|89167740|gb|CI021439.1|CI021439
EST:     TTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: TTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|89174516|gb|CI110714.1|CI110714
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|33654619|gb|CF277233.1|CF277233
EST:     CGAGAACATTAATAA-TTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|3761241|gb|C98489.1|C98489
EST:     AAGTTTCTGGCGCGAGCCCATTAATAATTTTGAAGAAAATGATTTNCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGC
genomic: AAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTT-CCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGC
EST: gi|38483054|gb|CF966856.1|CF966856
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATC
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATC
EST: gi|29688877|gb|CB685152.1|CB685152
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|88225670|gb|CI225586.1|CI225586
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|58679771|gb|CK068458.1|CK068458
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|58684033|gb|CK072720.1|CK072720
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|11442551|gb|BF430454.1|BF430454
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATTGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|88845531|gb|CI084456.1|CI084456
EST:     AATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: AATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|88250300|gb|CI348530.1|CI348530
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGC
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGT-GTGCTTATGACAATCATCGACACATCGGCCGACACGACTGC
EST: gi|8856617|gb|AU093935.1|AU093935
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTAAGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|88834129|gb|CI000493.1|CI000493
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|88964579|gb|CI069927.1|CI069927
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|33663504|gb|CF294471.1|CF294471
EST:     GAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: GAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|3764148|gb|AU030648.1|AU030648
EST:     CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: CAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|86870697|gb|CI323573.1|CI323573
EST:     TTGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: TTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
EST: gi|86908059|gb|CI298812.1|CI298812
EST:     TGAAGAAAATGATTTCCAG                         ATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT
genomic: TGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCT

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: 73 (upstream exon), 73 (downstream exon)
Score: 76

GCAACAAGTTCTTCTTGGCCATCTTGACTGGTCTCCAATGCACAAAGACCCAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttg ... atttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCTCTTGCTGTCGCCTGCTATGACCTCTCACAGTTCCTTCAGTACCACCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggactcaaacataaatattttgaaataacaccgtcaactttcaatttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCTCTTGCTGTCGCCTGCTATGACCTCTCACAGTTCCTTCAGTACCACCCTT
                        aaataac  putative branch site (score: 76)
                                              tttttgc  putative PPT
      tcaaacataaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaaacaaatgaaaaccctaatttatctgtaatttttttaagtagtggactcaaacataaatattttgaaataacaccgtcaactttcaatttttgcagATTCTACGTGTGCTTATGACAATCATCGACACATCGGCCGACACGACTGCTCTTGCTGTCGCCTGCTATGACCTCTCACAGTTCCTTCAGTACCACCCTT

-tcaaaca
- -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaca