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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGACATGCTACGTCGGCAATCTCTCCGCCCAGACCACATTAAGATGTTTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttctgaccagcccattattctgctataatacctccaacagtttgtatggctgatcttttacattatgtcttctgtagtgttcatgtttgtgtaa...

Basic information

species Oryza sativa
transcript LOC_Os02g05330.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
GTTTGACATGCTACGTCGGCAATCTCTCCGCCCAGACCACATTAAGATGTTTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttctgaccagcccattattctgctataatacctccaacagtttgtatggctgatcttttacattatgt---cttctgtagtgttcatgtttgtg-taa---
||  |||||| | ||  || |  | || ||| | |||  ||| |||   |||||||||||||| || ||||||||||| || || || || |||||||||||    ||| |  | |    |    | |    | | | ||   |||   | ||||  |   ||  |   | | |   | |||||  ||  |  || ||   | |   
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgta---ttccgttcggtgt-tggagcagggggattgcatcacgcag---ggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctggaatgaggg

upper sequence: LOC_Os02g05330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
GTTTGACATGCTACGTCGGCAATCTCTCCGCCCAGACCACATTAAGATGTTTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttctgaccagcccattattctgctataatacctccaacagtttgtatggctgatcttttacattatgtcttctgtagtgttcatgtttgtgtaa
 |  || |||||  | || |   | || || || ||| |||| ||||||||||| ||||| || || || |||||||| ||||| ||||||||||| |||||  | |       |  |   |  | |   |  |  |  ||      |||| || |  |                                         
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggt-ctatataaccaccctgcctgtgccttgtgtgtcgcag----------------------------------------
















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|29642250|gb|CB647257.1|CB647257
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|29666181|gb|CB662456.1|CB662456
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTC
EST: gi|33381553|gb|CF196896.1|CF196896
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|58664159|gb|CK052845.1|CK052845
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCAGCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|701121|gb|D47412.1|D47412
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|33381782|gb|CF197125.1|CF197125
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|58670852|gb|CK059538.1|CK059538
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|58680815|gb|CK069502.1|CK069502
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|29666180|gb|CB662455.1|CB662455
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCA
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCA
EST: gi|218498174|gb|FG949778.1|FG949778
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|29644972|gb|CB649979.1|CB649979
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCAC-AAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|29684184|gb|CB680459.1|CB680459
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTC
EST: gi|33795013|gb|CF323385.1|CF323385
EST:     TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAG-TCGGGAGTGTT
genomic: TTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGG-AGTGTT

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), 71 (downstream exon)
Score: 106

GTTTGACATGCTACGTCGGCAATCTCTCCGCCCAGACCACATTAAGATGTTTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttct ... cccttttcagATCTATGATATCTTCCAGCTCCTTCCACCAAAGATCCAGGTCGGAGTGTTCTCTGCTACCATGCCTCCTGAGGCCCTTGAGATCACCCGCAAGTTCATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGACATGCTACGTCGGCAATCTCTCCGCCCAGACCACATTAAGATGTTTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttctgaccagcccattattctgctataatacctccaacagtttgtatggctgatcttttacattatgtcttctgtagtgttcatgtttgtgtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccagccc