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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaagctaatacttccttgccttcagcatatatttaagcagtgatctaattctgtgtaatggtaaacatgtggatagtaaggtcaacaactttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAATTGTTCTTGGAGGTTGAACTTGGACTG

Basic information

species Oryza sativa
transcript LOC_Os07g06950.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G018508_T01 (Zea mays), 3'ss of exon 13
-----gtcaagc-taatacttccttgccttcagcatatatttaagcagtgatctaattctgtgtaatggtaaacatgtggatagtaaggtcaacaactttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAATTGTTCTTGGAGGTTGAACTTGGACTG
      | ||   |     ||  |||  || |||   || ||   |  ||  ||  |  ||| |       || | |    |  ||| |   |  | ||| | ||||||||||||||||| |||   |  || ||||| || ||||| ||| | |||||||||||||| |||||||||||||||
actcaattaactgtgggggtttattg--ttgagctgctactt---ctatg-ccttctcttgtctgtaaaggaataggccagttctaaaggagagcattttatatagGTTGGACAGCTAAAGGAATTGGTGAACAAGGCCCACAACGCTGAATTGAAATTGTTCTTGGAAGTTGAACTTGGACTG

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 13
--gtcaagctaatacttccttgccttcagcatatatttaagcagtgatctaattctgtgtaatggtaaacatgtggatag--taaggtcaacaactttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAATTGTTCTTGGAGGTTGAACTTGGACTG
    ||||     ||  |  ||  || |   | |  ||      ||| ||    ||| |||||        |   |  ||  |    | |   |   ||   ||| ||  |||||  |||    |       |  |   |       ||||   ||  |  | | | |              
tgaacaaggcc-cacaacgctgaattgaaattgttcttggaagttgaacttggactg-gtaataacttctttcctgtgagcctttatttatttaaggtgcagAGGGTGTTCAGCTGCAAGCCAAAATTTGCCACTCCTCTGTTAGGCAACTTTGATCATAGTAGTAAG--------------

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 19
gtcaagctaatacttccttgccttcagcatatatttaagcagtgatctaattctgtgtaatggtaaa----catgtggatagtaaggtcaacaactttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAATTGTTCTTGGAGGTTGAACTTGGACTG
   ||   |||      | |  || |   |  |  |    | |  | |   | |   | |  |||||    |||   | |  ||| |   |  |  || |||||||||| |||||||| |||   |  || ||||| || ||||||||||| ||| |||||||||| |||||||||||||||
---aactcaatttactgtggggtttattgttgagctgc-tacttctatgccttttcatcactgtaaaggagcattccggttctaaaggagagcatgttatgtagGTTGGGCAGCTAAAGGAACTGGTGAACAAGGCCCACAACGCAGAACTGAAACTGTTCTTGGAAGTTGAACTTGGACTG

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|33676384|gb|CF304623.1|CF304623
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|27577375|gb|CB000070.1|CB000070
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|58667338|gb|CK056024.1|CK056024
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|27576479|gb|CA999173.1|CA999173
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|29630971|gb|CB635980.1|CB635980
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGC
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGC
EST: gi|58693780|gb|CK082467.1|CK082467
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|33796382|gb|CF324058.1|CF324058
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|27576636|gb|CA999330.1|CA999330
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|58693799|gb|CK082486.1|CK082486
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|58668120|gb|CK056806.1|CK056806
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|33674888|gb|CF303127.1|CF303127
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
EST: gi|33674863|gb|CF303102.1|CF303102
EST:     ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACA                         GTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA
genomic: ATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAA

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: 75 (upstream exon), 74 (downstream exon)
Score: 29

TATTCCTACCCAATTTCAAAGATTTTGGCTGTGGGCCAAGCGACAAAACCATACATACCGGCCTAACCGTCCACTGACTCCTCAAGAAGAGACGCACACAgtaagatgaa ... ctttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAATTGTTCTTGGAGGTTGAACTTGGACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaattctgtgtaatggtaaacatgtggatagtaaggtcaacaactttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAATTGTTCTTGGAGGTTGAACTTGGACTG
 atctaat  putative branch site (score: 29)
                  taaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaagctaatacttccttgccttcagcatatatttaagcagtgatctaattctgtgtaatggtaaacatgtggatagtaaggtcaacaactttgtgtagGTTGGACAGCTAAAAGAAGCAGCAAATAAGGCTCATAACGCAGAACTAAAATTGTTCTTGGAGGTTGAACTTGGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - tgccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgg