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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagaaactgttgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT

Basic information

species Oryza sativa
transcript LOC_Os02g40890.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G125556_T03 (Zea mays), 3'ss of exon 2
attagaaactgttgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT
 |||       || ||  ||     |      | ||      |      | |        |    | || || ||      |   | |  | | |||||| |  |||||||||  |||| |||||||| ||||| ||||| |  ||||||||||| ||| |||||| | | ||||| |||||||||||||| ||||||||
cttaactgtatttctgttatgcaaataatagaaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT

upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G060870_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------attagaaactgttgtgggatcagtgtctctttagtgaattagtgtggattttt----gtttgctac------ggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT
                                                || |  |   || | || |    || | |  |   |   |   ||   |||     ||||||  |      ||  |||  |||||   |||  ||| ||    || ||| |  | ||||||| ||||| |||||||| ||||| ||||| || ||||||||||| ||| |||||| | | ||||| |||||||||||||| ||||||||
gtaattacacgtttatatacgtatttgcctaatgaatacgatattttttttggcaaaattattgggtgtacgtgtgtacaccaatacaccatgtcctttactcggtttgcccctcattgggatgatgggttgatatatttgttgattc---tttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT

upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G125556_T02 (Zea mays), 3'ss of exon 1
attagaaactgttgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT------
 |      ||||| ||  |  | |        | ||      |      | |        |    | || || ||      |   | |  | | |||||| |  |||||||||  |||| |||||||| ||||| ||||| |  ||||||||||| ||| |||||| | | ||||| |||||||||||||| ||||||||      
-tgtatttctgttatgcaaataatag-----aaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcaggttcagAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGTCTGCAA

upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G060870_T02 (Zea mays), 3'ss of exon 1
---attagaaactgt-tgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT
   ||||     |||  ||| |  ||      |   |     ||     || ||     |   |  ||  |||  |||||   |||  ||| ||    || ||| |  | ||||||| ||||| |||||||| ||||| ||||| || ||||||||||| ||| |||||| | | ||||| |||||||||||||| ||||||||
aaaattattgggtgtacgtgtgtacaccaatacaccatgtcctttactcggtttgcccctcattg-ggatgatgggttgatatatttgttgattc---tttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT

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|88728115|gb|CI751625.1|CI751625
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88313720|gb|CI597351.1|CI597351
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88315500|gb|CI615372.1|CI615372
EST:     ATCGACCGGGTCTCTGGTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|33662438|gb|CF293405.1|CF293405
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88312983|gb|CI592267.1|CI592267
EST:     GCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: GCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|66914261|gb|CX101109.1|CX101109
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGGCAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88423687|gb|CI617039.1|CI617039
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|33807484|gb|CF329619.1|CF329619
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|2429002|gb|C73465.1|C73465
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGA-                         NTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88347065|gb|CI631145.1|CI631145
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|396941507|gb|HO188716.1|HO188716
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|58680738|gb|CK069425.1|CK069425
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCTGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|33657911|gb|CF280525.1|CF280525
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88345773|gb|CI631041.1|CI631041
EST:     ATNGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGANAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88350631|gb|CI631354.1|CI631354
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTACAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88353482|gb|CI631667.1|CI631667
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|396941616|gb|HO188273.1|HO188273
EST:     CGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGGGCGAG                         CTATAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: CGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88719529|gb|CI743039.1|CI743039
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88343436|gb|CI621804.1|CI621804
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCGGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88692204|gb|CI735779.1|CI735779
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|86596781|gb|CI286694.1|CI286694
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88396738|gb|CI620071.1|CI620071
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88439220|gb|CI604505.1|CI604505
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGA
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88347123|gb|CI631203.1|CI631203
EST:     ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: ATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
EST: gi|88720933|gb|CI744232.1|CI744232
EST:     GGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAG                         CTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC
genomic: GGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGC

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), 75 (downstream exon)
Score: 23

ACTCCACCTCGGGTGAAAGCCGGCGCCTTTTGGATCACCCCTCTCCTCCGATCGACCGGGTCTCTGCTGAGGTCTCCACGCCGCCGACAGGTAGCGCGAGgtaaggggga ... tctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT
                         tgttgac  putative branch site (score: 23)
                                       ttgttttct  putative PPT
                                          ttttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagaaactgttgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG