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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccagaatctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC

Basic information

species Oryza sativa
transcript LOC_Os01g01710.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
gaattgaatgct-tgctgaagttctgta-tgcatgcaaactacattaccagaatc--tggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
 | |||||   | ||  |  | | |||  ||||| |||| || || | ||   |     |      | ||||| |||  |||||  |||  |||| ||||  |||||||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |
-atttgaacattatgtggttgctttgtgctgcat-caaa-taaatgagcaattttatcagtgaatatagctgacttggttacttgtattg-tttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 5
gaattgaatgcttgctgaagtt--ctgtatgcatgcaaactacattaccagaat-ctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
 || | |||| |  |||   ||   |   ||||  || | || || | ||   | |  |      | | ||  | |   ||||    || |||| ||||| |||||||||||||||||||||||||||| ||||| ||||||||||| |||||||| || |||||||||||||||||||| ||||||||||||||||| || |
-aagttaatg-taactgggtttggtttggtgcacccaga-taaatgagcaatttaccagtgaatatagttgtctcggtaactttgtattgtttgttctgctagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAAACGCTTATTGCAGGTGGTCCTTTCGTGCTTCCCCTTGCACACAAAC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccaga-atctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
| ||   |     |   |    ||   |  ||      |   ||  |||  ||| | || ||  |  |     ||  |  |   | || ||  | ||  |||| |||||||| || || ||||| |||||||| ||||| ||||| |||||||||||| | ||||| || ||||||||||| ||||| ||||| || ||||
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagttatcagacaacagatattagaaagctgaaatcc-tctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 5
gaattgaatgcttgctgaagtt-ctgtatgcatgcaaactacattaccaga-atctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
   || |   |      |||   ||   |  |       | ||||  ||   ||| | || ||  |  |     ||  |  |   | |  ||  | |   |||| ||||||||||| || ||||| |||||| | ||||| || || |||||||||||| | ||||| || ||||||||||| ||||| ||||| || ||||
-gtttaagaacacagaaaagacactaactaaagatggtattcattgtcacttatcagacaacagatattagaaagctgaaatcc-tcttattattttattagCCAACAGTTGCTGCGATAGAAGCAGGGAAATACATAGCTTTAGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 5
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccagaatctggcaccac----ttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
        |   | ||  | || | | |  ||  ||||   ||||  || || ||  |  |     |||| |||       |||     |  ||  |    |||||||| ||||||||||||||||| || || || || ||  | || |||||||||||| | || |||||||||||||| |||||||| |||||  | || |
-------gtatatactctaattttttgt-tat-taaaccttattaagaggatatgaaaaaagaaagttgcagatgataaagcttgttgcttatttttactgcagCCTACGGTTGCTGCAATTGAAGCAGGAAAGGACATTGCTCTTGCAAACAAAGAGACATTAATCGCAGGTGGTCCTTTCGTGCTTCCGCTTGCCAACAAAC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 5
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccagaatctggcaccacttgctgatttg----cctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
   |||| |   |  | |||  ||   |  ||| |||  |    |  |||| ||    | |  ||    | ||      | |||   | ||| |  |     |||||||||| |||||||| ||||| |||||||| ||||| || || ||||||||||| || ||||| || ||||||||||| ||||| |||||||| ||||
tccttgattttcttattaaggact---taaatgtaaataattggataagaaactaat-caagatgacagtctgaaaattttcttctgtgtctgtttttcattagCCTACAGTGGCTGCAATAGAAGCAGGGAAAGACATAGCCTTAGCCAACAAAGAGACCCTAATTGCTGGGGGTCCTTTTGTCCTTCCTCTTGCACACAAGC

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
gaattgaatgcttgctgaagttctgtatgcatgcaaacta-cattaccagaatctggcaccacttg--ctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
   |  | | ||   |  || |||  ||  |     || |  |||| ||| |  ||  | |  |||  |    ||   || || ||  | | |    ||| |||| ||||||||||| ||||||||||| |||||||| || ||||| |||||||||||  | ||||| || ||||| | |||| | || || ||  | ||||
--gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgc-agCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC

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|38474648|gb|CF958781.1|CF958781
EST:     C-GATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGACAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58607529|gb|CK035562.1|CK035562
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58689337|gb|CK078024.1|CK078024
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGA
EST: gi|33676538|gb|CF304777.1|CF304777
EST:     AGATGCAGTTACAGTTGTTACTGGGATAGTAGGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: AGATGCAGTTACAGTTGTTACTGGGATAGTAGGG-TGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29613664|gb|CB618677.1|CB618677
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29620639|gb|CB625650.1|CB625650
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29688464|gb|CB684739.1|CB684739
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29681868|gb|CB678143.1|CB678143
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58696138|gb|CK084825.1|CK084825
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29617049|gb|CB622061.1|CB622061
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58669161|gb|CK057847.1|CK057847
EST:     GTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: GTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29620626|gb|CB625637.1|CB625637
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|29620641|gb|CB625652.1|CB625652
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|33381852|gb|CF197195.1|CF197195
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCNNNACTGANG                         NCTACAGTTGCTGCAATTG
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTG
EST: gi|58688021|gb|CK076708.1|CK076708
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58694512|gb|CK083199.1|CK083199
EST:     CTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
EST: gi|58589270|gb|CF987578.1|CF987578
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTG
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTG
EST: gi|58690161|gb|CK078848.1|CK078848
EST:     CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA
genomic: CAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAA

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), 68 (downstream exon)
Score: 52

GTTGCTCGCCACCCAGATGCAGTTACAGTTGTTACTGGGATAGTAGGGTGTGCAGGACTGAAGgtaatctttc ... gctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagaatctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC
                  tgctgat  putative branch site (score: 52)
                                      tttctttgctctgcc  putative PPT
                              tacttaaatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattgaatgcttgctgaagttctgtatgcatgcaaactacattaccagaatctggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC

- - - - tgcttgc
- - - - - - - - - - ttctgta
- - - - - - - - - - - - - -tgcatgc
- - - - - - - - - - - - - - - - - -aactaca
- - - - - - - - - - - - - - - - - - - - - - accagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ctggcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctac