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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGAGAAGATGTGCTTCGTGCAGCTCATCATCCCCGCCGAGAGCGCGCGCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctctctctctctatctctcgctctcggcgccagtcgctgcccgcatcagaggcccctctctccctcccggatctgtgtgatctagcctcgtgaa...

Basic information

species Oryza sativa
transcript LOC_Os01g61780.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61780.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G879240_T01 (Zea mays), 5'ss of exon 1
GTCCGAGAAGATGTGCTTCGTGCAGCTCATCATCCCCGCCGAGAGCGCGCGCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctctctctctctatctc-tcgctctcggcgccagtcgctgcccgcatcagaggcccctctctccctcccggatctgtgtga-tctagcctcgtgaa----------
||||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||| || |||||||||||||||||||||  | ||| |||| ||||  ||||| | ||  |     ||  |||| || |        |  || | |||||||||  |||| || ||||||| |            
GTCCGAGAAGATGTGCTTCGTGCAGCTCATCATGCCCGCCGAGAGCTCGCGCCTCGCCGTCACCTACCTCGGCGAGCTCGGCCTACTCCAGTTCAAGGACgtgagtgcccctccctctctctcgccgctccctgctac-----ctcaccgcctctgg-------ccttctcgcccggatctacgtgaatccagcctcgagtcgtggtctctc
















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|88368677|gb|CI658309.1|CI658309
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88396314|gb|CI598426.1|CI598426
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88368744|gb|CI646226.1|CI646226
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88339186|gb|CI633757.1|CI633757
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88582562|gb|CI699980.1|CI699980
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88719573|gb|CI743083.1|CI743083
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|163921035|gb|EG710411.1|EG710411
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88720621|gb|CI743920.1|CI743920
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88334309|gb|CI642554.1|CI642554
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88327614|gb|CI646807.1|CI646807
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88333502|gb|CI656574.1|CI656574
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88351023|gb|CI620683.1|CI620683
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88288664|gb|CI663453.1|CI663453
EST:     GCCTCGCCGTCACCTACCTCGGNGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTT
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTT
EST: gi|88368745|gb|CI646227.1|CI646227
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88395114|gb|CI609430.1|CI609430
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88329706|gb|CI650174.1|CI650174
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
EST: gi|88729638|gb|CI751441.1|CI751441
EST:     GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCACTTCAAGGAC                         TTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG
genomic: GCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG

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: 55 (upstream exon), 45 (downstream exon)
Score: 10

GTCCGAGAAGATGTGCTTCGTGCAGCTCATCATCCCCGCCGAGAGCGCGCGCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctct ... ttatatgcagTTGAATGAGGATAAGAGTCCTTTTCAGCGTATATTTGTCAATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGAGAAGATGTGCTTCGTGCAGCTCATCATCCCCGCCGAGAGCGCGCGCCTCGCCGTCACCTACCTCGGCGAGCTCGGGCTCCTCCAGTTCAAGGACgtgagtctctctctctctatctctcgctctcggcgccagtcgctgcccgcatcagaggcccctctctccctcccggatctgtgtgatctagcctcgtgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cggcgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc