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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccaatttcatgtattaaggccgcagctctcttgtgaagctgtagtttcacatgccatcctgtttgtaaatataaactgaaaccattagtcctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g21250.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G314679_T02 (Zea mays), 3'ss of exon 4
--------gccaatttcatgtatta-aggccgcagctctcttgtgaagctgtagtttcacatgccatcctgtttgtaaatataaactgaaaccattagtcctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG
        |     | |||| | || | |  |||| || || |  |   |||  |||   |     | |||     ||||   || |       |  |  || |||||| || || ||||||||||||||||| |||||||| || |||||||||||||||||||||||||||||||  ||||| |||||||||
gtgttacagattgctccatggagtagaagttgcag-tcactagccactttgttttttttgacaatgtactg-----aaat---aatttgggttttgtgcacttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAATGCTGTTGATGGTTCTGTGCCCTTTTCTGAGCAG
















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|88517568|gb|CI445222.1|CI445222
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|89198260|gb|CI015649.1|CI015649
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGTCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|8955503|gb|BE229309.1|BE229309
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|86506579|gb|CI149212.1|CI149212
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88485774|gb|CI423045.1|CI423045
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88281898|gb|CI403294.1|CI403294
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88277852|gb|CI398654.1|CI398654
EST:     GAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|86831266|gb|CI297535.1|CI297535
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|86526502|gb|CI166708.1|CI166708
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88277867|gb|CI398669.1|CI398669
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88511151|gb|CI438657.1|CI438657
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88277106|gb|CI397908.1|CI397908
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGGTTGCAACCA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGG-TTGCAACCA
EST: gi|163928617|gb|EG711178.1|EG711178
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88520651|gb|CI448305.1|CI448305
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88243238|gb|CI244360.1|CI244360
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88483987|gb|CI421258.1|CI421258
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|86522432|gb|CI162638.1|CI162638
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|117248583|gb|CT862782.1|CT862782
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|163927524|gb|EG709956.1|EG709956
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88964103|gb|CI033020.1|CI033020
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88281682|gb|CI403078.1|CI403078
EST:     GAGAATCT-GAC-TGATACTTCTCTGCATCGATGAAATT-TAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
EST: gi|88491507|gb|CI428779.1|CI428779
EST:     GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG                         CATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA
genomic: GAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAA

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: 58 (upstream exon), 75 (downstream exon)
Score: 38

GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGGgtaatggttt ... cctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacatgccatcctgtttgtaaatataaactgaaaccattagtcctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG
                                            tcctcctgc  CT-rich tract
               tgtttgtaaatataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccaatttcatgtattaaggccgcagctctcttgtgaagctgtagtttcacatgccatcctgtttgtaaatataaactgaaaccattagtcctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - -tttcatg
- - - - - - - - - - ccgcagc
- - - - - - - - - - - - - - - cttgtga
- - - - - - - - - - - - - - - - - - - gctgtag
- - - - - - - - - - - - - - - - - - - - - - - - - catgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccat