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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttccacatgctatgaaaaggcatttcattccagccaaatgaaaattattttctagtggtgctatagtggtatatattttcaagagtgaggtac...

Basic information

species Oryza sativa
transcript LOC_Os08g29720.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G106703_T02 (Zea mays), 5'ss of exon 9
AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttccacatgctatgaaaaggcatttcattccagccaaatgaaaat-tattttctagtggtgctatagtggtatatattttcaagagtgaggtac
   |||||  ||||||||||||| ||||| ||||||||||| ||| |||| || |||||||| |       |    |   |||||  |    |       |||       |  ||||  || ||  | | |  |||| |   |||| || | | | |   
---GATACTGAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaattcctcattcccaaaagataaagtagcatgctcaatgagctgtacatttgttattgtggttgtgttggtttcagttttgaacactaatgat-

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G059018_T01 (Zea mays), 5'ss of exon 9
AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttccacatgctatgaaaaggcatttcattccagccaaatgaaaattattttctagtggtgctatagtggtatatattttcaagagtgaggtac---
||||||||  | ||||||||||| ||||| |||||||||||||||||||| || |||||||| |       |        ||||     || |    |||    |  |     | |   | || |  | | || || |   |||||| |  |||        
AAGGATACTGAGAAGGCAATGAGGATGACTACAAGGCAAACATTAGCTGAGATATGGAGgtaaggaaatacctcatccccaaaata---tttaaagtagcatgtttgatgggctgtataattgctattgtggttgtgttggttttcaggtttgaaccctaca

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G106703_T01 (Zea mays), 5'ss of exon 9
AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttccacatgctatgaaaaggcatttcattccagccaaatgaaaat-tattttctagtggtgctatagtggtatatattttcaagagtgaggtac
||||||||  ||||||||||||| ||||| ||||||||||| ||| |||| || |||||||| |       |    |   |||||  |    |       |||       |  ||||  || ||  | | |  |||| |   |||| || | | | |   
AAGGATACTGAAAAGGCAATGAGGATGACTACAAGGCAAACGTTAACTGAGATATGGAGgtaaggaaattcctcattcccaaaagataaagtagcatgctcaatgagctgtacatttgttattgtggttgtgttggtttcagttttgaacactaatgat-

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|66925835|gb|CX112683.1|CX112683
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|29646262|gb|CB651269.1|CB651269
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86522457|gb|CI162663.1|CI162663
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|87007018|gb|CI275326.1|CI275326
EST:     TGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: TGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86494625|gb|CI137258.1|CI137258
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86499881|gb|CI142514.1|CI142514
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTATTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|87015826|gb|CI279578.1|CI279578
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|29639863|gb|CB644872.1|CB644872
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|29661211|gb|CB657486.1|CB657486
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86500551|gb|CI143184.1|CI143184
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86502542|gb|CI145175.1|CI145175
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86859418|gb|CI278837.1|CI278837
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|29680568|gb|CB676843.1|CB676843
EST:     CAAAAGGCAATGAGAATGTCCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86493384|gb|CI136017.1|CI136017
EST:     CAAAAGNCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|87019187|gb|CI277903.1|CI277903
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|88244722|gb|CI243844.1|CI243844
EST:     GGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: GGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86539697|gb|CI179903.1|CI179903
EST:     ACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: ACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|29677505|gb|CB673780.1|CB673780
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86600100|gb|CI258440.1|CI258440
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|86494335|gb|CI136968.1|CI136968
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|33683082|gb|CF311321.1|CF311321
EST:     AAAAGGCAATGAGAATGACCACAAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAA-G---GTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: AAAAGGCAATGAGAATGACCAC-AAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|88197385|gb|CI196692.1|CI196692
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|25807715|gb|CA763676.1|CA763676
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCCCCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
EST: gi|88228108|gb|CI227588.1|CI227588
EST:     CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAG                         CTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG
genomic: CAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACG

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: 59 (upstream exon), 74 (downstream exon)
Score: 76

AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttc ... aacctggcagCTCTGGAGGTATGAAAGGCTTGTTCACCGGTGTTGGTCCACGTGTAGCACGAGCTGGCCCATCAGTTGGAATCGTCATTTCTTTCTACGAGGTTGTGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGATACGCAAAAGGCAATGAGAATGACCACAAGGCAAACATTAGCTGATATTTGGAGgtatgtcttccacatgctatgaaaaggcatttcattccagccaaatgaaaattattttctagtggtgctatagtggtatatattttcaagagtgaggtac

- - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG