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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatttacctttttgttggcaatacaatatatatctcattttattctttcatgtttctattagaatcattactctctttttacatcactataactctatccttatgccaacaaactgaaaagacgcttgttatggcagtag

Basic information

species Oryza sativa
transcript LOC_Os10g38980.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38980.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G162251_T02 (Zea mays), 5'ss of exon 6
AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatttacctttttgttggcaatacaatatatatctcattttattctttcatgtttctattagaatcattactctctttttacatcactataactctatccttatgccaacaaactgaaaagacgcttgttatggcagtag
|||||||  ||||||| ||||||||| |||| | ||| | |||||||||||||||||||||  ||| | |    | |    || ||     |||   || ||        ||  |     |||  | ||||    | |                                                        
AAATGTCGCTGCCTGCTTTGCCTGTCTCGCCGAAATCAGAAAGCTCAGgtacttaatttacaattt-gcttctgagatgtcatctact--gtttccatccttagcaaacttaacatgcatatttttttcttcgcccgtag------------------------------------------------------

upper sequence: LOC_Os10g38980.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G162251_T01 (Zea mays), 5'ss of exon 5
AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatttacctttttgttggcaatacaatatatatctcattttattctttcatgtttctattagaatcattactctctttttacatcactataactctatccttatgccaacaaactgaaaagacgcttgttatggcagtag
|||||||  ||||||| ||||||||| |||| | ||| | |||||||||||||||||||||  ||| | |    | |    || ||     |||   || ||        ||  |     |||  | ||||         |  ||  ||  |||  |                                     
AAATGTCGCTGCCTGCTTTGCCTGTCTCGCCGAAATCAGAAAGCTCAGgtacttaatttacaattt-gcttctgagatgtcatctact--gtttccatccttagcaaacttaacatgcatatttttttcttcgc------ccgtaggtccctccaga-------------------------------------
















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|86500464|gb|CI143097.1|CI143097
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         GTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGA
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtagGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGA
EST: gi|116875026|gb|EC365534.1|EC365534
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|116875026|gb|EC365534.1|EC365534
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|116875026|gb|EC365534.1|EC365534
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|29666973|gb|CB663248.1|CB663248
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         GTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGA
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtagGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGA
EST: gi|86504223|gb|CI146856.1|CI146856
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|88283178|gb|CI404624.1|CI404624
EST:     AGAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AGAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|88482069|gb|CI419340.1|CI419340
EST:     TCATTGCCTGCATTCCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: TCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|86861783|gb|CI329548.1|CI329548
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|88522672|gb|CI449489.1|CI449489
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|88555527|gb|CI485792.1|CI485792
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|88466556|gb|CI532363.1|CI532363
EST:     AATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGGTCAGTAG                         GTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCG
genomic: AATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagtagGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCG
EST: gi|88522247|gb|CI449992.1|CI449992
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|88552657|gb|CI482685.1|CI482685
EST:     ATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGGCTCAGTAG                         GTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTGTATTCTTTGCG
genomic: ATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAA-GCTC---AGgtacttaatt ... atggcagtagGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCG
EST: gi|88537263|gb|CI465088.1|CI465088
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt
EST: gi|116875033|gb|EC365541.1|EC365541
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|116875033|gb|EC365541.1|EC365541
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|116875033|gb|EC365541.1|EC365541
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|29640850|gb|CB645857.1|CB645857
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|29640850|gb|CB645857.1|CB645857
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|29640850|gb|CB645857.1|CB645857
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         T
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtag-
EST: gi|88483086|gb|CI420357.1|CI420357
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG                       
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AGgtacttaatt ... atggcagt

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), 49 (downstream exon)
Score: 5

AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... atggcagtagGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGACGGCCATCACCTTCTGAGAAATGCTTCACCTAGTGAACCAGGAGCTTCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatttacctttttgttggcaatacaatatatatctcattttattctttcatgtttctattagaatcattactctctttttacatcactataactctatccttatgccaacaaactgaaaagacgcttgttatggcagtag

- - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - -  AGCTCA