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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcctgttccatccttcttcccccatttctttctgctacactaataacttcttcacttgcattgcgccttgttcccaacacatgccatatccaagatgaactatccgtgttggatgtagaggccgggtttttaatccattatatatatataaaggatgaaccatgatatcatcttccatttttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g38840.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 14
gtacgtcctgttccatccttcttcccccatttctttctgctacactaataacttcttcacttgcattgcgccttgttcccaacacatgccatatccaagatgaactatccgtgttggatgtagaggccgggtttttaatccattatatatatataaaggatgaaccatgatatcatcttccatttttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
                              | | |  || | || |  || | |  || || ||  |     ||||| ||| ||||| |  |   |    ||||     | || |||||| ||        ||    |  |||  ||  ||||||            | | | |     | || ||||  ||||||||||||| || ||||||||||| ||||||||||| || |||| |
-----------------------------gtgcgtgatgttcca-tcctatcctagtc-ctagcgctaaat-ttgtttccagcacattcagttctc----tgaaa----cttgctggatgaagcaattc--ttccccagtcatggta-gtatatat-----------tcacacccctgactatgttttc-acagGATAAGAGGAGACCAGCAGCACTTCGTTCGCCGAGATGAGCTGAGG
















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|88219092|gb|CI220365.1|CI220365
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|86862356|gb|CI345349.1|CI345349
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88273363|gb|CI388819.1|CI388819
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88275573|gb|CI396177.1|CI396177
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88245497|gb|CI245346.1|CI245346
EST:     TACCTAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88996866|gb|CI389532.1|CI389532
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88518045|gb|CI445598.1|CI445598
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|86432491|gb|CI086102.1|CI086102
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88472832|gb|CI410103.1|CI410103
EST:     CAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: CAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|89176067|gb|CI043088.1|CI043088
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|86843192|gb|CI341351.1|CI341351
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88256221|gb|CI358609.1|CI358609
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|89180521|gb|CI044800.1|CI044800
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88517913|gb|CI444802.1|CI444802
EST:     AAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: AAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88237644|gb|CI237493.1|CI237493
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|86535002|gb|CI175208.1|CI175208
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88376598|gb|CI537902.1|CI537902
EST:     TATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88516425|gb|CI444079.1|CI444079
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTNTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88262014|gb|CI365590.1|CI365590
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCACCAGCACTCTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|89192387|gb|CI049848.1|CI049848
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88420370|gb|CI559616.1|CI559616
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|29616737|gb|CB621749.1|CB621749
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|89190198|gb|CI392248.1|CI392248
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88845594|gb|CI084519.1|CI084519
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88478723|gb|CI415994.1|CI415994
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88409040|gb|CI556748.1|CI556748
EST:     CGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: CGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|89178707|gb|CI391705.1|CI391705
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88257654|gb|CI360240.1|CI360240
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|218492006|gb|FG967745.1|FG967745
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCNGCAGCACTTTGTTCGCCGAGACGAACTGAAT
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|89177186|gb|CI043689.1|CI043689
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88242908|gb|CI240759.1|CI240759
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88447385|gb|CI544259.1|CI544259
EST:     GTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: GTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88540877|gb|CI468953.1|CI468953
EST:     GTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: GTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88537565|gb|CI466523.1|CI466523
EST:     TGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88460847|gb|CI552983.1|CI552983
EST:     GACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: GACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88487048|gb|CI424319.1|CI424319
EST:     GACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: GACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
EST: gi|88531486|gb|CI459965.1|CI459965
EST:     TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATAC                         GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
genomic: TACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG

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), 46 (downstream exon)
Score: 15

TAGAAATGGCAACCGAACAAAGCGAGCTGGATCTGTCATATGGGCTACGCTACCAAGACGTGAAGATCCCAGAAGCGTATGAACGCCTCATCCTGGATACgtacgtcctg ... tttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattatatatatataaaggatgaaccatgatatcatcttccatttttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG
                                 tcatcttccatttttt  CT-rich tract
     atatatatataaagga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtcctgttccatccttcttcccccatttctttctgctacactaataacttcttcacttgcattgcgccttgttcccaacacatgccatatccaagatgaactatccgtgttggatgtagaggccgggtttttaatccattatatatatataaaggatgaaccatgatatcatcttccatttttttgacagGATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG