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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgtcgattcccaaatttagtatttgtagatagactttgtttggtattacttggttacctgtcacttaatgtcaaatcttaacataaggataac...

Basic information

species Oryza sativa
transcript LOC_Os04g30760.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g30760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G351023_T01 (Zea mays), 5'ss of exon 3
GTCCTGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgtcgattcccaaatttagtatttgtagatagactttgtttggtattacttggttacctgtcacttaatgtcaaatcttaacataaggataac---
|| ||||| || ||||| || || || |||||||||||||| |||||||||||||||||| |||| |||| ||||||     ||  ||| ||   |||||||      |  |   ||   |  |  |   |    ||    | || |   ||||   
GTTCTGGTAAATTATGCTCGGTCTTCGAAAGAGGCTGAAGAGGTCTCCAAAGAGgtgagcatgtccattcacaaatt--actttgttaggtattatttgtttctctgaaactctatagaagcaatattgcggtgcataacca-attatcgtaactgt

upper sequence: LOC_Os04g30760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G099696_T01 (Zea mays), 5'ss of exon 3
GTCCTGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgtcgattcccaaatttagtatttgtagatagactttgtttggtattacttggttacctgtcacttaatgtcaaatcttaacataaggataac------------------
|| ||||| ||||||||||| ||||| |||||||||||||| |||||||||||||||||| |||  |||| ||||||                ||||| || ||||||| ||||||  |||  ||||  | |  ||     |||||  || ||                   
GTTCTGGTAAACTATGCCCGGTCCTCGAAAGAGGCTGAAGAGGTCTCCAAAGAGgtgagcatgtgcattcgcaaatt----------------actttattgggtattatttggttctctgaaactt--tttagaaagcagacatagagacaatcagccgtgcagtcgtgca
















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|14980713|gb|BI305391.1|BI305391
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|23514981|gb|BU673887.1|BU673887
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|30227133|gb|CB965025.1|CB965025
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|30227817|gb|CB965709.1|CB965709
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|23512833|gb|BU672855.1|BU672855
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|30226632|gb|CB964524.1|CB964524
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|30227770|gb|CB965662.1|CB965662
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|30228838|gb|CB966729.1|CB966729
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|23514324|gb|BU673583.1|BU673583
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
EST: gi|23513544|gb|BU673187.1|BU673187
EST:     TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAG                         ATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA
genomic: TGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAA

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: 74 (upstream exon), 70 (downstream exon)
Score: 66

GTCCTGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgt ... atttttccagATCGAAGCATGTGGTGGTCAGGCTATTACCTTCGGGGGAGATGTTTCAAAAGAAGCCGATGTGGATTCTATGATGAAAGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTGGTGAACTATGCCCGATCCTCAAAAGAGGCTGAAGAAGTCTCCAAAGAGgtgagcttgtcgattcccaaatttagtatttgtagatagactttgtttggtattacttggttacctgtcacttaatgtcaaatcttaacataaggataac

- - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - AGAAGT