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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTTCGTAACACCTTCAGATTCGGTTGCCATTATTGCAGCCAATGCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgtaatcctgcatattaagctgcagataacccctgcacttttctggtttacaattttttttaatgggggcttttaagttgcatactgcattcac...

Basic information

species Oryza sativa
transcript LOC_Os03g50480.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 11
ATTCTTCGTAACACCTTCAGATTCGGTTGCCATTATTGCAGCCAATGCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgtaatcctgcatattaagctgc--agataacccctgcacttttctggtttacaattttttttaatgggggcttttaagttgcatactgcattcac
|||||| || ||||| || || || ||||||||||| || |||||||||||||| || |||||||||||| |||||||||| ||||||||||||||||| || |   |||| ||||||  |||||  | |||||  ||  |  | | |    |  ||    | | | || ||||    |||  | |  |  || |   
ATTCTTTGTGACACCATCGGACTCTGTTGCCATTATAGCGGCCAATGCTGTTCAATCAATTCCTTACTTTGCTTCTGGCCTGAAGGGAGTTGCCAGgtaaaaagctctcctccatattgtgctgctaatataacatctagatatatttttactgtaagaactctcactgtgggcacc-aagcggtaagcaccactgc-

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 11
ATTCTTCGTAACACCTTCAGATTCGGTTGCCATTATTGCAGCCAATGCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgtaatcctgcatattaagctgcagataacccctgcacttttctggtt--tacaattttttttaatgggggcttttaagttgcatactgcattcac
|||||| || ||||| || || || ||||||||||| ||||||||||||||||| || |||||||||||| |||||||||| ||||||||||||||||| || ||  |||| ||||||  |||||  |||   | |  || | | | |||   | ||    |   | ||  ||||   | |  | |  || || |   
ATTCTTTGTGACACCGTCGGACTCTGTTGCCATTATCGCAGCCAATGCTGTTCAATCAATTCCTTACTTTGCTTCTGGCCTGAAGGGAGTTGCCAGgtaaaaagttctcctccatattgtgctgctaatatgacatctacatatattgttaccataaaaactcccactgtaggctcc-aggcggtaagcttcactgc-
















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|58663537|gb|CK052223.1|CK052223
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58695799|gb|CK084486.1|CK084486
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCC
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCC
EST: gi|55438389|gb|CV732490.1|CV732490
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|45244957|gb|AB118181.1|AB118181
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58604743|gb|CK015271.1|CK015271
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58663518|gb|CK052204.1|CK052204
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58596192|gb|CK006720.1|CK006720
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58596286|gb|CK006814.1|CK006814
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|218492308|gb|FG946716.1|FG946716
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|163918448|gb|EG711618.1|EG711618
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|33380770|gb|CF196113.1|CF196113
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58670270|gb|CK058956.1|CK058956
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACAATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATC
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACA-TCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATC
EST: gi|2428319|gb|C72782.1|C72782
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58671485|gb|CK060171.1|CK060171
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|29689390|gb|CB685665.1|CB685665
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58604363|gb|CK014891.1|CK014891
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
EST: gi|58601534|gb|CK012062.1|CK012062
EST:     GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAG                         GAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT
genomic: GCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCT

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), 64 (downstream exon)
Score: 208

ATTCTTCGTAACACCTTCAGATTCGGTTGCCATTATTGCAGCCAATGCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgta ... aaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCTCAAGTTCTTTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTTCGTAACACCTTCAGATTCGGTTGCCATTATTGCAGCCAATGCTGTTCAGTCGATTCCTTACTTTTCTTCTGGCCTTAAGGGAGTTGCCAGgtacaatgtaatcctgcatattaagctgcagataacccctgcacttttctggtttacaattttttttaatgggggcttttaagttgcatactgcattcac

- - - - - - - - - - - - - - - - - - - - - - - GCTGTT