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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g48960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031827_T05 (Zea mays), 3'ss of exon 1
gttaccagataagccattcatatacatatatataga-agcacttcttgagatttggacaataaattctgacaattttttt----taatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
           |  | || ||   |||   | | || | ||   | |||| ||    |       | | ||  | | ||     | ||  | || ||   ||    | |||  |||||||      |||     | ||||||||||||| |||||||| || ||||| || |||||||| ||||| |||||||| ||||||||||||        
-----------attccttgatccccatggttcttgataacaggccatgagtttataccccctccatttcaccttatattgaagatgatactattcttgcttatgcttgaagGTTGTCAGTCTGCAAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031827_T06 (Zea mays), 3'ss of exon 1
gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
  ||     | | ||   |||     |  |||      ||    || | |      | ||     || | | ||     | ||  | || ||   ||    | |||  |||||||      |||     | ||||||||||||| |||||||| || ||||| || |||||||| ||||| |||||||| ||||||||||||        
-gtattccttgatcc--ccatggttcttgataacaggccatgagtttataccccctccatttcaccttata-ttgaagatgatactattcttgcttatgcttgaagGTTGTCAGTCTGCAAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031827_T02 (Zea mays), 3'ss of exon 1
gttaccagataagccattcatatacatatatatagaag--cacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG----------------
               || |  ||   | |  |||  ||  ||    || | |      | ||     || | | ||     | ||  | || ||   ||    | |||  |||||||      |||     | ||||||||||||| |||||||| || ||||| || |||||||| ||||| |||||||| ||||||||||||                
---------------atccccatggttcttgataacaggccatgagtttataccccctccatttcaccttata-ttgaagatgatactattcttgcttatgcttgaaggttgtcagTCTGCAAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGCTTGTCGTC

upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025014_T01 (Zea mays), 3'ss of exon 2
---gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
   | | | |||||| | |  |||     || ||  |  | | | |||    || |   ||    ||  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
catggttctagataa-caaaccatgagtttacat-cattatcccctct----atct---caccttatattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
------------------gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
                  | | | |||||| | |  |||     |||||  |  | | | |||    || |   ||     |  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
gtattccttgatccccatggttctagataa-caaaccatgagtttatat-cattatcccctct----atct---caccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020928_T03 (Zea mays), 3'ss of exon 2
---gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
   | | | |||||| | |  |||     |||||  |  | | | |||    || |   ||     |  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
catggttctagataa-caaaccatgagtttatat-cattatcccctct----atct---caccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
gttaccagataagccattcatatacat-atatatagaagcacttcttgagatttggacaataaatt-ctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG----------------
         |      || || |   | |||| ||  |     | || |  ||  | | |||  || || |  || || || |||   |  | | | |  | |||| |     || ||| |  |      | |||||||||||||||||||||||| ||||| |||||||| || || || || ||||| || |||||||||                
-----ttagtttcttgttgatgtttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgact--gatttcttaaactcagG-----GTGGAAATTCT------GCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC

upper sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTT---TGAAAGTCATGGCGGAGCATTTGGCT--TCAATATTTGGGACTG-AGAAGGATAGGGTTAACTGCCCCTT-TTACTTCAAG
 || | | |||     ||||   ||  || | |  ||       | || |||  | ||           || ||   || |||||||  | ||   | |     || || | |||   | | |   | ||  |    ||    | |   | |   |  |  | | | ||  | ||   |      | || |||     | ||||   
-ttgctaaatatcttgttcaatgactgatttcttaaactcagggtggaaattctgccat---ggcggagcatttggcttcaatcttt--ggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT-

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|88761779|gb|CI771335.1|CI771335
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|88589118|gb|CI706972.1|CI706972
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|86850550|gb|CI309362.1|CI309362
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|29686176|gb|CB682451.1|CB682451
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|2312597|gb|C28752.1|C28752
EST:     AGCGNGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAG-ATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|88395759|gb|CI590774.1|CI590774
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|88593254|gb|CI709416.1|CI709416
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|88314829|gb|CI608288.1|CI608288
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|88851921|gb|CI679479.1|CI679479
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|86847645|gb|CI288750.1|CI288750
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|86830466|gb|CI291944.1|CI291944
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|88361273|gb|CI626377.1|CI626377
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
EST: gi|86876913|gb|CI309724.1|CI309724
EST:     AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: AGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC

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: 56 (upstream exon), 72 (downstream exon)
Score: 71

GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAGgttcgtgttc ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG
                                     tctttttgtt  CT-rich tract
            aataaattctgacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG

- - - - - - gccattc
- - - - - - - - - - - - - - - - - - - - cttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caataaa