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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttatattttatttttgtctgtattgtgtataggtcatggtcacatacacacatcacactaatatctaacaagtgtatgaagtaatttatgcttcctttatgcctatgttctttctaaatggctaatccttgccatcccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAATGGTTCATTGTCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACAC

Basic information

species Oryza sativa
transcript LOC_Os02g58340.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 12
gtatgttttatattttatttttgtctgtattgtgtataggtcatggtcacatacacacatcacactaa-tatcta-acaagtgtatga--agtaatttatgcttcctttatgcctatgttctttctaaatggctaatccttgccatcccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAATGGTTCATTGTCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACAC
                                   |  | |  | ||||| |    |     |  |   |  ||| |||| | ||| |  ||||||  ||||  | ||    | | ||||  |||||                     ||  |||||||||| ||||| ||||| || |||||||| ||||| | ||| || || ||||| ||| |||||||||||||||| |||| ||||||||| || || ||||
----------------------------------cactgcttcttgtcacctttgaatgctgccttttctgcctatacaattatataaggagtaatccatgc--cattccaacttctgtttcttcta---------------------ctcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC
















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|87010666|gb|CI312358.1|CI312358
EST:     TGTCGCTGCAAAGAATTTTCCCGTGGCTGGCACCTTCAAGTTTACGTCAG                         ATACGGTTTTGGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAA
genomic: TGTCGCTGCAAAGAA-TTT-CCGT-GCTGGCACCTTC-AGTTTACGTCAGgtatgtttta ... ccttctgcagATAC-GTTTT-GCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAA
EST: gi|29685086|gb|CB681361.1|CB681361
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|29628315|gb|CB633326.1|CB633326
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|29629259|gb|CB634270.1|CB634270
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|86497160|gb|CI139793.1|CI139793
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|58587575|gb|CF985883.1|CF985883
EST:     AGCTTGTCTCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|87040458|gb|CI195080.1|CI195080
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|87036488|gb|CI191110.1|CI191110
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|87041614|gb|CI196236.1|CI196236
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|27577497|gb|CB000192.1|CB000192
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|66912656|gb|CX099504.1|CX099504
EST:     AGCTTGTCTCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|38471500|gb|CF955631.1|CF955631
EST:     AGCTTGTCTCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|313084093|gb|HO213876.1|HO213876
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
EST: gi|9864982|gb|AU100732.1|AU100732
EST:     AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAG                         ATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT
genomic: AGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAAT

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: 70 (upstream exon), 60 (downstream exon)
Score: 37

TGCAAAGCATTATGAAACAGGCGAACTTCTTCCAGAGGAAATTTATGCAAAGCTTGTCGCTGCAAAGAATTTCCGTGCTGGCACCTTCAGTTTACGTCAGgtatgtttta ... ccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAATGGTTCATTGTCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttatgcctatgttctttctaaatggctaatccttgccatcccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAATGGTTCATTGTCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACAC
                                  tccttgccatcccttc  CT-rich tract
                   tttctaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttatattttatttttgtctgtattgtgtataggtcatggtcacatacacacatcacactaatatctaacaagtgtatgaagtaatttatgcttcctttatgcctatgttctttctaaatggctaatccttgccatcccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAATGGTTCATTGTCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACAC

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