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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgcaatgagttattgttttactcatactgctagatgatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG

Basic information

species Oryza sativa
transcript LOC_Os02g35470.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 5
gtatgtttgcaatgagttattgttttactcat--actgcta----gatgatttgaatgtt-----actcgt--------taaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
   | | ||  ||   || ||| |||||||||    || ||    ||| |  || || ||     ||| |          || |||  |  |  ||||| |   |||||||||||| ||||| |||||  | || ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||
--gtatgtgtgatacattgttgatttactcattagatgatacaaagattacgtgtattttttagaacttgcatcagttgcaagcatgctgattctgtatttattagTGTACAAAAAACACTACCCACCCACGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGG

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
gtatgtttgcaatgagttattgttttactcat--------------actgctag-atgatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
   | | ||  |     | ||| |||||||||              | | |  | ||  || |||| |   |||  || |||  |  | |||||| |   ||||||||| |||||||| |||||||| || ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||
--gtatgtgtgacacactgttgatttactcattagatgaaacaaagattacctgtatttttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
gtatgtttgcaatgagttattgttttactcatactgctagatgatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
               || | |   | |     | || |  ||| ||  |   ||  ||  |||  ||| || || |  |  ||||||| ||||| |||||||| ||||||||| | || ||||| || |||||| | || |||||||||||||||||| | || ||||| | | |||||  |   ||
---------------gtaagtacataaacttcattgttt-atg-ttctatccttcttctgtaatgatacttatacttga--ttgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtttgcaatgagttattgttttactcatactg--ctagatgat-ttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
||||| |   ||  || |    ||||  ||  ||||  | |  || | || | |  |  | |||      |  | | || ||| | ||||||||||| ||||| ||||||||||| || || |||||||| |||||||| || ||||| ||||||||||| |||||||| || ||| | | |||    ||
gtatggtcttaa-aagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgt-gcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
------------------gtatgtttgcaatgagttattgttttactcatactgctagatg-----atttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
                    |  ||   | | | || || || ||     |    |   ||      || | ||| |  | || || |  |    |  | | | |  |||| ||||| |||||||| || |||||  | || ||||| |||||| |||| || ||||||||||| |||||  |||||||||||| ||| |||  |  |||
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
------------gtatgtttg-caatgagttattgttttactcatactgctagatgatttgaatgtta---ctcgttaaccatatttctattgtatcttg--cagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
              ||  ||| |  | | ||||||  ||| |  || || |   |   ||   ||| |   |  ||||   |   | || || |  | ||   |||||| || || ||||||||||||||  |||  |||||||| |||||||| || |||||||||||||||||| |||||||||||| | |||||        
gtaggttcaggctcatccttgtcttttatttattgaattattt-tattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------gtatgtttgcaatgagttattgttttactcatactgctaga-tgatttgaatgttactc--gttaaccatatt---tctattgtatct----------tgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
                                                              ||| || | |||| | ||||||  ||       | |    ||||||| ||  ||  | |     ||||   ||| || ||  |          |||||||||||| |||||||||||||||||| | || || || || ||| | || || |||||||| ||||| || || || ||||||    | |||  ||    
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtt-tcgttttaggcagttaataaaagcagtttgaatatttatctagatggaagtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4
------------gtatgtttgcaatgagtt-attgttttactcatactgctagatgatttgaatgttactcgttaaccatatttctattgtatcttg--cagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG-
             |   || |   || | | | ||   |  |  ||     |||  | |   || |   |   |||  ||  || |     | ||||  |||| ||||| ||||||||||| |||||  |||| || || |||||| |||| || |||||||| || || ||||| ||||||||     ||||| ||||    
tgccctgtgcacatccattcgttctgtgctgaatgccgtgat--taacagaagaaaaatcatatctctatatctaataattgttgttggtcaccttgtacagTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAAT-CAAGCAAG

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtatgtttgcaatgagttattgttttactcatactgctagat--gatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG-
                | |||| ||  |   ||       |  ||  | || |||  |||   |    |    |||  |  | |    |   | || ||||||||||||||||||||| ||||||||| | || || || || ||| | || || |||||||| || |||||||| |||||||||    | ||| ||||    
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagc--atggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAAT-CAAGCCAA

upper sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4
----gtatgtttgcaatgagttattgttttactcatac-----tgctagatgatttgaatgttactcgttaaccatatttctattg--tatcttg--cagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
      |  ||| |||   || ||      |   |        || |  | |      || |   |  ||     ||||  | |||  ||   ||  |||| ||||| |||||||||||||| ||| | || || || |||||| |||| || |||||||| || || ||||| |||||||||    |||||  |  |  
tctgccagatttccaagttgtgatcagaagaagaaagaagggatggtgaaagcccaacatatctgtatttttgattattgttgttgattactctgttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA

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|29662458|gb|CB658733.1|CB658733
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|86877077|gb|CI311412.1|CI311412
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGGTGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|29675099|gb|CB671374.1|CB671374
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTT
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTT
EST: gi|29674900|gb|CB671175.1|CB671175
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|29677880|gb|CB674155.1|CB674155
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTANAGGATGATGTTTGG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGG
EST: gi|58677698|gb|CK066385.1|CK066385
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|29628697|gb|CB633708.1|CB633708
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|29630082|gb|CB635091.1|CB635091
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAG
EST: gi|29680200|gb|CB676475.1|CB676475
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|66924740|gb|CX111588.1|CX111588
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|33796937|gb|CF324332.1|CF324332
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|29626070|gb|CB631081.1|CB631081
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|33675030|gb|CF303269.1|CF303269
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
EST: gi|29629686|gb|CB634695.1|CB634695
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAA
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAA
EST: gi|33380769|gb|CF196112.1|CF196112
EST:     TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAAT                         TGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG
genomic: TAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAG

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: 74 (upstream exon), 73 (downstream exon)
Score: 54

TTCAGGCTTGGGCTGAGGGTTGCCCCAGGGTCTTTTGAAGGTATTCGTGTTAGGGAGGCGAAGACAGAAGCTTTTACTGTTAAGGATCACAGAGGGGAATgtatgtttgc ... tatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctagatgatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG
                         cgttaac  putative branch site (score: 54)
                                 atatttctattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttgcaatgagttattgttttactcatactgctagatgatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT