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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtgcaaatattgggaggtttgtgatgcaatgcaatttatctttatcctaattgaacgacattcatgtttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCATATGATATT

Basic information

species Oryza sativa
transcript LOC_Os04g09860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g09860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G101250_T02 (Zea mays), 3'ss of exon 3
------------------------gtggtgcaaatattgggaggtttgtgatgcaatgcaatttatctttatcctaattgaacgacattcatgtttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCATATGATATT
                        ||  ||||  |           ||  |  || |||||||| |  |  |  ||| | ||  | | | ||| || | |||||||||||||||||||||| ||| ||||||||||||||||||||||||| ||||||||||||
gtgatgcttataagggttatgcttgta-tgcaggtccccttcaaagtgctacacattgcaattt-taatctttttaagtaaataagagttatgcttgtatgcagATGCTCAACTGCCATGCTACTTCATCGCAGAATGCAGAGCGGGAGAGTGCATATGATATT
















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|88332583|gb|CI651743.1|CI651743
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88335917|gb|CI645518.1|CI645518
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88308695|gb|CI653582.1|CI653582
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88338766|gb|CI660537.1|CI660537
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88341777|gb|CI642921.1|CI642921
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88361061|gb|CI646085.1|CI646085
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|58693762|gb|CK082449.1|CK082449
EST:     GGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: GGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88377794|gb|CI637928.1|CI637928
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|58601435|gb|CK011963.1|CK011963
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88346448|gb|CI637294.1|CI637294
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|58678266|gb|CK066953.1|CK066953
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88573821|gb|CI665590.1|CI665590
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88664834|gb|CI701384.1|CI701384
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|29634037|gb|CB639046.1|CB639046
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88726267|gb|CI749922.1|CI749922
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88305179|gb|CI651976.1|CI651976
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88731371|gb|CI754984.1|CI754984
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88330185|gb|CI658490.1|CI658490
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88592435|gb|CI710537.1|CI710537
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88341776|gb|CI642920.1|CI642920
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88717504|gb|CI741014.1|CI741014
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|29643625|gb|CB648632.1|CB648632
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88294215|gb|CI667189.1|CI667189
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88328228|gb|CI651236.1|CI651236
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|88574595|gb|CI666364.1|CI666364
EST:     ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA
EST: gi|66932263|gb|CX119111.1|CX119111
EST:     ATATCACTCAGCGGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAG                         ATGCTCAACTGCCATGCAACTCCATCGCANAATGCAGAGCGGGAGAGGGCA
genomic: ATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCA

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: 51 (upstream exon), 46 (downstream exon)
Score: 12

GTTCGCAAGTCAGGATGTTCCATTCAATATACCGCACTGCATTGCTCGACATATCACTCAGCAGAAGGATGATACACCAAGGCTTTCTGTGCGAGACAAGgtggtgcaaa ... ttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCATATGATATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcaatgcaatttatctttatcctaattgaacgacattcatgtttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCATATGATATT
                      tcctaat  putative branch site (score: 12)
                                            tttattt  putative PPT
          aatttatctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtgcaaatattgggaggtttgtgatgcaatgcaatttatctttatcctaattgaacgacattcatgtttatttgcagATGCTCAACTGCCATGCAACTCCATCGCAGAATGCAGAGCGGGAGAGGGCATATGATATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG