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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaatacttccctcatttttttattgcgtaacttctctctttttaagttcttatgaggtgtattttgttcacatatgagtcctatattttgcgacatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA

Basic information

species Oryza sativa
transcript LOC_Os03g17710.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G099317_T02 (Zea mays), 3'ss of exon 3
-------------------gtatgtg-aatacttccctcatttttttattgcgtaacttctctctttttaagttcttatgaggtgtattttgttcacatatgagtcc-tatattttgcgacat-ctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA
                    || ||  ||| |       ||||   |  || || |   |   ||| |||  ||  |  ||    |||||| |  |   |||  | | || ||||||     | | |  |||||| |||||| |||||||| |  |||||||| |||||||| |||||  | ||||||||||||||||| |||||||| |||||| ||||||||||||||||||| 
gtacgttatttttacctccctaagtttaattcagtagctatttacattctgtgttatagcatacttgttat-tttgtgggaaacatattttttatatgcatggtttcgtacattttgttctgttccaaattaccatacagGAGTTCAGTGAACATCGTGATGCCGATGAAGCTCGGTACCAACTAGATGGCAGGGATGTCGATGGAAGTCGCATTGTTGTTGAGTTTGCTAAAGGG

upper sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G35980.4 (Glycine max), 3'ss of exon 3
-----------------------gtatgtgaatacttccctcatttt---tttattgcgtaacttctc-----tctttttaagttctta-tgaggtgtattttgtt-cacat------atgagtcctatatt----ttgcgacatctattttacca------aacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA
                        ||| |    | |||  |   |||   ||| ||  |||  | ||      |   ||  |||  ||  |  |  | |||  |||  | ||      |||| | || | ||    |   | | | |   |||| |        ||||| || |||||||| || ||||||||||| ||  | |||||||| |||||  |||||||||||||||| || ||| |||| || ||||| ||||| 
gtaagttgtcaccctttctttgtctatttattgatttcttttgatttcaatttcttatgtatttgcttaaaagtggcttctagtatttgctttgaggaattcagttgtagatgatggaatgatttctgtgttactttcttggcttgttcgttacaacttttgggcagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGG

upper sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G33260.1 (Glycine max), 3'ss of exon 3
-------------------------------------------gtatgtgaatacttc--cctcatttt-tttattgcgtaacttctctctttt--taagttcttatgaggtgtattttgttcaca----tatgagtcctatatt----ttgcgacatctattttacca------aacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA
                                            | |   |  |||||    || | || ||||||   |||  | |  ||| |  ||  | |||    |   |   ||||  |      ||||| | || | ||    |   | | | |   |||| |       |||||| || |||||||| || ||||||||||| ||  | |||||| | |||||  |||||||||||||||| || ||| |||| || ||||| ||||| 
gtaagttgtcaccctttctttatctttgtctatttatttatttatttcctaggacttcaatttcttcttatttatttgctaaaatgtggcttctagtatctgcttggaggaattcagttgtagatgatggtatgatttctgtgttactttcttggcttgttccttacaacctttggacagGATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG

upper sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
-----------------gtatgtgaatacttccctcatttttttattgcgta------------acttctctctttttaagttcttatgaggtgtatt----------ttgttcacatatgagtcctatattttgcg-----acatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA
                 ||   |  ||   |  |   ||| |   |||| ||            | || |||| || |   |   ||  ||    |||          ||   || |||||||       || | ||      ||  || |||     ||||||||||||||||||||| ||||||||||| ||  | |||||| || ||||  | ||| |||||||||| || ||  |||| || ||||| ||||| 
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG

upper sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ22951 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgaatacttccctcatttttttattgcgtaacttctctctttttaagttcttatgaggtgtattttgttcacatatgagtcctatattttgcgacatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA
               | ||   ||| |  | ||||    |||| | |||    |||| ||    |   ||||||  | | |      |  ||||  |    || | |||  | | ||||||||||| |||||||| ||||||||||| ||| || || | ||  | ||  ||||  | || |||  ||||||  | || |||||||| | | | 
--------------acttcgcctttgttgtacgtagaaactctttcttttctctcttttgct-cgctctttgttttctttt--tctattcatttctctctttcgagtttcgcta-cagGAATTCAGCGATCCCCGGGATGCTGATGAGGCGAGGCATTATCTCAACGGACGGGACTTCGAGGGACACCGCATGATCGTCGAGTTTGCGAGAAGG

upper sequence: LOC_Os03g17710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ30580 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgaatacttccctcatttttttattgcgtaacttctctctttttaagttcttatgaggtgtattttgttcacatatgagtcctatattttgcgacatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA
     | ||      | ||   ||| |  | ||||    |||| | |||   | ||       ||| || | ||   || | | | || | ||| | |       |||  | |  ||||||||||| |||||||| ||||||||||| ||| || || | ||  | ||  ||||  | || |||  ||||||  | || |||||||| | | | 
-----tcaagcacgacttcgcctttgttgtacgtagaaactctttcttt---tgctcgctctttgttttctttttctat-tcacttctctctttcgag-------tttcgcta--cagGAATTCAGCGATCCCCGGGATGCTGATGAGGCGAGGCATTATCTCAACGGACGGGACTTCGAGGGACACCGCATGATCGTCGAGTTTGCGAGAAGG

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|33654664|gb|CF277278.1|CF277278
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88422877|gb|CI615177.1|CI615177
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|58673537|gb|CK062223.1|CK062223
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATACCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|58602955|gb|CK013483.1|CK013483
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATACCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|58653740|gb|CK042420.1|CK042420
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATACCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88573286|gb|CI664857.1|CI664857
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|33654208|gb|CF276822.1|CF276822
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88327495|gb|CI646681.1|CI646681
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88729424|gb|CI752934.1|CI752934
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|66917360|gb|CX104208.1|CX104208
EST:     AATACGTGAAGTGGAGTTGAAGCGCCACTACGCGTCTTATT                         GAATTCAGTGATCCC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGT-TTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCC
EST: gi|218497275|gb|FG960321.1|FG960321
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATACCCGTGATGCTGATGAAGCGCGGTATAACCTAACATGG
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAG-ATGG
EST: gi|88572064|gb|CI663635.1|CI663635
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|109974555|gb|DT806973.1|DT806973
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATACCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88349704|gb|CI632839.1|CI632839
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTACATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|58674796|gb|CK063483.1|CK063483
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATACCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88328329|gb|CI651340.1|CI651340
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|117220967|gb|CT861417.1|CT861417
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATACCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88720424|gb|CI743723.1|CI743723
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88761659|gb|CI771215.1|CI771215
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88424660|gb|CI606459.1|CI606459
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCACGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
EST: gi|88342002|gb|CI644339.1|CI644339
EST:     AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATT                         GAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGC

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: 49 (upstream exon), 72 (downstream exon)
Score: 34

AATACGTGAAGTGGAGTTGAAGCGCGACTACGCGTTTATTgtatgtgaat ... taccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattttgttcacatatgagtcctatattttgcgacatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA
                                      tctatttt  CT-rich tract
                                     atctatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaatacttccctcatttttttattgcgtaacttctctctttttaagttcttatgaggtgtattttgttcacatatgagtcctatattttgcgacatctattttaccaaacagGAATTCAGTGATCCCCGTGATGCTGATGAAGCGCGGTATAACCTAGATGGCAGGGATGTTGATGGAAGCCGCATTCTTGTTGAGTTTGCTAAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG