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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTACAAGTCAAATCCTCTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatacataaaatgttaggcatcttttggaaggatgctggatctatttcttttgaagaatggtttgatattttagatgatgaatctttgctcactattttgtgtag

Basic information

species Oryza sativa
transcript LOC_Os06g30060.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G341027_T02 (Zea mays), 5'ss of exon 3
GATTTACAAGTCAAATCCTCTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatacataaaatgttaggcatcttttggaa---ggatgctggatctatttcttttgaagaatggtttgatattttagatgatgaatctttgctcactattttgtgtag--
||||| ||||||||||| ||||||||| ||||| |  | ||||||||||| ||||| || ||||| |||||||   |        | ||      |||    ||     ||||    | | |    | |||    ||| |   |||| |   |  |     | |  | | |||||| | |    
GATTTGCAAGTCAAATCATCTCCACCATCTCAGTCGGCAACTTTACACAATGATCCTGCTATTATTCAGgtaaccttttgc----tatttcattacttgaaaaatttaaatgccttctgtgtgaagtatgagaggtggctcactattattattattattattattattattattttctttgcag
















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|38468847|gb|CF952978.1|CF952978
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTCGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|58607778|gb|CK035811.1|CK035811
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTTGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|58672585|gb|CK061271.1|CK061271
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTCGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|29623763|gb|CB628774.1|CB628774
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTTGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|29636795|gb|CB641804.1|CB641804
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|58667348|gb|CK056034.1|CK056034
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTCGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|117231418|gb|CT846842.1|CT846842
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTTGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|58674349|gb|CK063035.1|CK063035
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTCGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|29618259|gb|CB623271.1|CB623271
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTTGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
EST: gi|58601474|gb|CK012002.1|CK012002
EST:     CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAG                         TCACATTATCCTCGTGCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA
genomic: CTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACA

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: 69 (upstream exon), 65 (downstream exon)
Score: 55

GATTTACAAGTCAAATCCTCTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatac ... ttttgtgtagTCACATTATCCTTGTCCTGCCTCTACGAGCTTACCGCCTCCTGCAAGCACAGCAGCTGATCCTGCCTCACACAATGGTCAGTCAGGAATTCAGATGCCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTACAAGTCAAATCCTCTCCACCAGCTCAGCCTACTACTTTACACAACGATCCAGCGATTATCCAGgtaaatatacataaaatgttaggcatcttttggaaggatgctggatctatttcttttgaagaatggtttgatattttagatgatgaatctttgctcactattttgtgtag

- - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - AGCTCA