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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAAGAGAGCAGTATGTTAGAGCTTTATTTGTTCAGGCGGATGGTGTAAAACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttgagtcctgtaataataaccaaagctgaacttttctttccccaaattgctatattcttttccttgatataggatacatatatcaatttcctt...

Basic information

species Oryza sativa
transcript LOC_Os07g36470.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g36470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G163233_T01 (Zea mays), 5'ss of exon 8
GCTAAGAGAGCAGTATGTTAGAGCTTTATTTGTTCAGGCGGATGGTGTAAAACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttgagtcct--gtaataataaccaaagct-------gaacttttctttccccaaattgctatattcttttccttga--tataggatacatatatcaatttcctt------------------------------------------------------------
||||||||| |  ||||||||  | ||||||||||| || |||||  | || ||||||||||| |||||||| |||||| ||||||||||||| || |||||  ||| |  | |||  | |   | ||   ||          |||   || | ||   |  |   || ||  |  |  ||    | | |   |||   || || |   |                                                             
GCTAAGAGAACCATATGTTAGGACATTATTTGTTCAAGCTGATGGCATCAAGCTGCTCATTCCATTAATTTCCCCAGCTGCCACACAACAGTCAATTCAGgtgattgcttggccctaagcatctagaatggaaataccttggagaagagttgtctcattaggtgattagatcttagtagttcgattgttgacaacaggcataaactgtttcatctttcaaccctggaactaacttccacagctgtgttcctttttgttatttcttgtgcag

upper sequence: LOC_Os07g36470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G019999_T01 (Zea mays), 5'ss of exon 5
GCTAAGAGAGCAGTATGTTAGAGCTTTATTTGTTCAGGCGGATGGTGTAAAACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttgagtcct--gtaataataaccaaagct-------gaacttttctttccccaaattgctatattcttttccttgatataggatacatatatcaatttcctt------------------------------------------------------
||||||||| |  ||||||||  | ||||||||||| || |||||  | || ||||||||||| |||||||| |||||||||||||||||||| || |||||  ||| |  | |||  | |   | ||   ||          |||   || | ||  ||  |      | | |  |    ||||   || | | |        || ||                                                      
GCTAAGAGAACCATATGTTAGGACATTATTTGTTCAAGCTGATGGCATCAAGCTGCTCATTCCCTTAATTTCCCCAGCTTCCACACAACAGTCAATTCAGgtgattgcttggccctaagcatctagaatggaaatacgttggggaagagttgtctcatcaggtcttagcagtttgattgcagataacagacataaactgttccatctttcaactctagaactaacttcctcacctgtgttcctttttgttatttcttgtgcag
















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|2443142|gb|C74913.1|C74913
EST:     AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAG                         CTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
genomic: AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
EST: gi|38479045|gb|CF963178.1|CF963178
EST:     AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAG                         CTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
genomic: AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
EST: gi|38483054|gb|CF966856.1|CF966856
EST:     AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAG                         CTTCGTCGACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGC
genomic: AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTC-TCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGC
EST: gi|58691898|gb|CK080585.1|CK080585
EST:     AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAG                         CTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
genomic: AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
EST: gi|11442551|gb|BF430454.1|BF430454
EST:     AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAG                         CTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
genomic: AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
EST: gi|58682821|gb|CK071508.1|CK071508
EST:     AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAG                         CTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
genomic: AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
EST: gi|218495142|gb|FG957786.1|FG957786
EST:     CACAACAGTCGATCCAG                         CTTCTCTACGAAACTTGCCTCTGCATCTGGC-TTTATCCTTTTATGATGCC
genomic: CACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
EST: gi|58687201|gb|CK075888.1|CK075888
EST:     AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAG                         CTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA
genomic: AACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCA

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), 66 (downstream exon)
Score: 36

GCTAAGAGAGCAGTATGTTAGAGCTTTATTTGTTCAGGCGGATGGTGTAAAACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttg ... tcatttgcagCTTCTCTACGAAACTTGCCTCTGCATCTGGCTTTTATCCTTTTATGATGCAGCCGTTGATTATTTGTCCACTACAAGGGTTATGCCAAGACTTGTAGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAAGAGAGCAGTATGTTAGAGCTTTATTTGTTCAGGCGGATGGTGTAAAACTGCTCATTCCTTTAATTTCTCCAGCTTCCACACAACAGTCGATCCAGgtatttgttgagtcctgtaataataaccaaagctgaacttttctttccccaaattgctatattcttttccttgatataggatacatatatcaatttcctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttcccc