Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGATGCTCGGAAGGCCGCTCCGTGTGGCGACCCCTCACGCGGCGGCCCCCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttccagtgctgtttgttttctctcgtgatttctcgtctcgtgcgagagagagatttcgggttttaccgtctggagaaggatttttttttatctc...

Basic information

species Oryza sativa
transcript LOC_Os05g42350.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G090338_T01 (Zea mays), 5'ss of exon 1
---------GCGGATGCTCGGAAGGCCGCTCCGTGTGGCGACCCCTCACGCGGCGGCCCCCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttccagtgctgtttgttttctctcgtgatttctcgt--ctcgtgcgagagagagatttcgggttttaccgtctggagaaggatttttttttatctc
          ||| ||||||| |||||| |||| ||||||   || | ||| |||||||   | ||||| |      ||||  |||  ||||||||||||||||||||||||||| | |   |   || ||||     | |    ||  |    || |  |   | |   || ||||     || | |  ||  |    |   ||    | 
CCCGCGGTCCCGGGTGCTCGGGAGGCCGATCCGGGTGGCG---CCACCCGCCGCGGCCCGGCCGGGCGGTG------CGTCCGCGGGTAGCATACGCGCCGTCTCCGCGgtgagtctgcgtcg--attggtttcgagccttcgcctcgggagattcctcgggctggggcgttccgggcgccgccatttctaggggatcatgggttccgttt
















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|66919033|gb|CX105881.1|CX105881
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|24208531|gb|AU225558.1|AU225558
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|2309738|gb|C25893.1|C25893
EST:     C-NTGNGC-GCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CGCTG-GCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|58612442|gb|CK040154.1|CK040154
EST:     CCGCTGGCGGCGGCGGGTCGTGGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|86888169|gb|CI301861.1|CI301861
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|88588836|gb|CI706678.1|CI706678
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|33674915|gb|CF303154.1|CF303154
EST:     GGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: GGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|88352157|gb|CI613808.1|CI613808
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATTTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|29621654|gb|CB626665.1|CB626665
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|218494143|gb|FG961822.1|FG961822
EST:     CC-CTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|29625860|gb|CB630871.1|CB630871
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|88398900|gb|CI601236.1|CI601236
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGAG                         CCACTAAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|702026|gb|D48317.1|D48317
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGNCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGGATCAT
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAG-ATCAT
EST: gi|117230329|gb|CT842158.1|CT842158
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|12404888|gb|AU166489.1|AU166489
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|33380892|gb|CF196235.1|CF196235
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|87009000|gb|CI304943.1|CI304943
EST:     CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
EST: gi|88590034|gb|CI708861.1|CI708861
EST:     CGCCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCG                         CCACTCAAGAACGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC
genomic: CGC-TGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATC

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), 74 (downstream exon)
Score: 57

GCGGATGCTCGGAAGGCCGCTCCGTGTGGCGACCCCTCACGCGGCGGCCCCCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttcc ... gtgcctgcagCCACTCAAGAAGGATGCATCTGAAGTTAAGAGGAGCAAGGTTGAGATCATCAAGGAGAAGAGCAATTTTCTTCGGTACCCTTTGAATGAGGAACTGGTCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGATGCTCGGAAGGCCGCTCCGTGTGGCGACCCCTCACGCGGCGGCCCCCGCTGGCGGCGGCGGGTCGTCGTCGGCCAGCATACGCGCCGTCTCCGCGgtgagtttccagtgctgtttgttttctctcgtgatttctcgtctcgtgcgagagagagatttcgggttttaccgtctggagaaggatttttttttatctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagaagg