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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtaagtcttgcacttatcactggctggtccacttgtatttattgaatgcttgcatatgaaacacttatgatgcttttccaatacttgttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG

Basic information

species Oryza sativa
transcript LOC_Os05g07130.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 18
---------------------------------------------------------------------------------tgtgtaagtcttgcactt-atcactg-gctggtccactt--gtatttattgaa-tgcttgcatatgaaacacttatgatgcttttccaatacttgttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG
                                                                                  |||| || |      || ||  |   ||||  | | ||  | |   |  ||| ||     |    |||  ||| ||   ||| |  ||| |||||| ||||||| ||||| |||||||||||  ||||||| || ||||||||||||||||||||||| |||||||| |||||
gtacgtataaagaaaattttgctttattgttgtagttgcaccatgtgcatggaatatccgttacttaccattcatatatgaggtgttagaccaatgtttcatttccatgctgtacaaattaggaaaaaacagaaatgaaattaacacaaatccttttggcacttgtg-aatgcttgtttcaaccagGTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG

upper sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 19
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 19
------------------------tgtgtaagtcttgcacttatcactggctggtccacttgtatttattgaatgcttgcatatgaaacacttatgatgc-ttttccaatacttgttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG
                        | |||||       |  | | ||| || | |   |     |  |    |   |    | | | ||   | |    | | ||    | | | |  |  | ||||| || || |||||||||||| |||| |||||||| |||||||| || ||||||||||| || ||  |
gtaagtgacttgatcaaatccgtatatgtaatgtaaaaaagtgttactagcagctatcccctcgtagaacagaaaataaactctcagacttctctacctcatcttgtggtgcatatgactgc-agATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTACCTTGATGTAATCCAACG
















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|58611022|gb|CK038734.1|CK038734
EST:     CCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: CCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
EST: gi|29629510|gb|CB634519.1|CB634519
EST:     GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
EST: gi|29616012|gb|CB621024.1|CB621024
EST:     GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
EST: gi|29612782|gb|CB617795.1|CB617795
EST:     GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
EST: gi|29615977|gb|CB620989.1|CB620989
EST:     GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
EST: gi|88844562|gb|CI020409.1|CI020409
EST:     ATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: ATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
EST: gi|29615975|gb|CB620987.1|CB620987
EST:     GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
EST: gi|29616052|gb|CB621064.1|CB621064
EST:     GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA                         ATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA
genomic: GATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGAgtatgtgcta ... ttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgcttgcatatgaaacacttatgatgcttttccaatacttgttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG
           atatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtaagtcttgcacttatcactggctggtccacttgtatttattgaatgcttgcatatgaaacacttatgatgcttttccaatacttgttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - tcttgca
- - - - - - - - - - - -tggctgg
- - - - - - - - - - - - - - - - - cttgtat
- - - - - - - - - - - - - - - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacttg