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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctacaacattccgttcttctctcctcccgctcgcctgcggatctaaccgtgcgtgtgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA

Basic information

species Oryza sativa
transcript LOC_Os02g30050.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G043279_T03 (Zea mays), 3'ss of exon 1
gtaagctacaacattccgttcttctct------cctcccgctcgcctg---cggatctaaccgtgcgtgtgtggt--gcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
|||||| ||  |    | ||| || |       | ||  |||   |||   |   | |    ||| |    ||    |||||||| ||||||||  ||||||| |||||||||| |||| |||| |||||||| ||||||||||| || ||| | |||||||||||||||||||| |||||
gtaagccacctccaggctttcatcccaattaaacttcgagctgatctgacacccgttttgttgtgtggcgatgactggcagCCCGTATCAAGGTGCACGAGCTCCGGGGGAAGAGCAAGACGGACCTGCAGGCGCAGCTCAAGGAGCTGAAGTCTGAGCTCTCCCTCCTCCGCGTAGCCAA

upper sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G010599_T01 (Zea mays), 3'ss of exon 1
gtaagctacaacattcc-----gttcttctctcctcccgc-tcgcctg--cggatctaaccgtgcgtgtgtggt--gcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
||||||     | |||      ||   | ||   |  ||| ||| ||   ||||||| ||| |  || |  |||  |||||||||||||||||  ||||||| || || |||| |||| |||| ||||| || ||||||||||| || ||  |||||||||||||||| |||||||||||
gtaagcacatccgttctctctggtcactgtcgtttttcgcgtcgtctctccggatctgaccttctgttttcggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAGCGCAGCTCAAGGAGCTTAAATCGGAGCTCTCCCTCCTACGCGTCGCCAA

upper sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AC206642.4_FGT001 (Zea mays), 3'ss of exon 1
gtaagctacaacattccgttcttctctcctcccgctcgcctgcggatctaaccgtgcgtgtgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
|||||| ||  ||   | | ||    |  || | |||  |||   | ||  |  |    |  |   |||||||||||||||||  ||||||| |||||||||| ||||||||| ||||| || ||||| |||||  | ||| ||||||||||||| || ||||| |||||
gtaagc-acctcaactcctcctcgcatgttctctctcatctg---acctttctcttttcggtt--cgcagCCCGGATCAAGGTGCACGAGCTGCGGGGGAAGAGCAAGGCGGATCTGCAAGCGCAGCTTAAGGAGTTTAAGTCGGAGCTCTCCCTGCTACGCGTAGCCAA

upper sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G05270.1 (Glycine max), 3'ss of exon 1
------------------------------gtaagctacaacattccgttcttctctcctcccgctcg-cctg--cggatctaaccgtgcgtgtgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
                                |||   ||| |||      || | |  |  |    |  |||   | |  |||   |  |       || |||  |||| |||||  |||||||  ||   ||||  ||||||||||||| |  |||||| ||||| ||||||||||||||  |||| ||||||||||||||
gtaagactaagacaaagacattcattttaacgaagactcaaaattgttccattttttttttacatgtgatctgaatgaaattaaaattttgacgacactgaagCGAGGATAAAGGTTTACGAGCTTAGGAACAAGACGAAGGCGGAGCTGCTGAACCAGCTGAAGGATCTCAAGGCGGAGCTTGCCCTGCTCCGCGTCGCCAA

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|86599713|gb|CI253698.1|CI253698
EST:     CCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|86597406|gb|CI282530.1|CI282530
EST:     GCCCGCCGCGCCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: GCCCGCCGCGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|86424037|gb|CI062798.1|CI062798
EST:     CTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|88207400|gb|CI207249.1|CI207249
EST:     TCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: TCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|88240030|gb|CI239192.1|CI239192
EST:     GCCGCGCCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: GCCGCGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|86256752|gb|CI061515.1|CI061515
EST:     CGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|86855732|gb|CI269059.1|CI269059
EST:     TCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: TCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|38474903|gb|CF959036.1|CF959036
EST:     TCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: TCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|86423743|gb|CI062504.1|CI062504
EST:     CCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|88208864|gb|CI206715.1|CI206715
EST:     TCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: TCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|86257924|gb|CI064277.1|CI064277
EST:     CCGCGCCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CCGCGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|218502506|gb|FG953955.1|FG953955
EST:     CCCGCCGCGCCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CCCGCCGCGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|88204834|gb|CI202685.1|CI202685
EST:     CGCCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|218504163|gb|FG953017.1|FG953017
EST:     CGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|88244283|gb|CI243405.1|CI243405
EST:     TCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: TCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|88237000|gb|CI236849.1|CI236849
EST:     CGCCGCCCGCCGCGCCGCCTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CGCCGCCCGCCGCGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
EST: gi|88211581|gb|CI211221.1|CI211221
EST:     CCGCCCGCCGCGCCGCTTCCGTCGCCATGG                         CCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG
genomic: CCGCCCGCCGCGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGG

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: 43 (upstream exon), 75 (downstream exon)
Score: 46

TTCCCCTTCCTAGCACCGCCGCCGCCGCCGCCGCCGCCGCCGCCCGCCGCGCCGCCTCCGTCGCCATGGgtaagctaca ... tgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgttcttctctcctcccgctcgcctgcggatctaaccgtgcgtgtgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
                              atctaac  putative branch site (score: 46)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctacaacattccgttcttctctcctcccgctcgcctgcggatctaaccgtgcgtgtgtggtgcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC