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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgctacaagatttgatctattaagactaacgatgttttacagtagtacttcttagttctagcagttagtgttgtatttcgcttttcctattgtat...

Basic information

species Oryza sativa
transcript LOC_Os04g02820.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g02820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AC203173.3_FGT004 (Zea mays), 5'ss of exon 1
GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgctacaagatttgatctattaagactaacgatgttttacagtagtacttcttag--ttctagcagttagtgttgtatttcgcttttcctattgtat-----
         |||||||||||||||| ||||||||| ||    || |||||||| ||||| ||||||||||| |||||||| ||||||||||| ||||||||||||| | |  |    |  | | |||    | |    ||  |    || || || | ||  |  | |   |||   || ||||||| |||   | ||  |      
---------ATGGTGAAGTTCACGGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAATATGTCTGTTATTGCTCATGTGGACCATGgtatgttcaa--aacactactttgttagatgttatatagtcct----taatatttttgagcctctttgtttttaaaatt-tatttcgttttcaatgtttaagagcta

upper sequence: LOC_Os04g02820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G113250_T01 (Zea mays), 5'ss of exon 2
GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgct--acaagatttgatctattaagactaacgatgttttacagtagtactt---cttagttctagcagttagtgttgtatttcgcttttcctattgtat
|  | |||||||||||||||||| | ||||||||| ||    || |||||||| ||||| |||||||||||||||||||| ||||||||||| |||||||||| || |   |||       |   |||  ||       |||| |     | || ||   ||| || ||     | | ||  | ||    || ||| |  |    
GGAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTTATTGCTCATGTGGACCATGgtaggttcagaacactgcccaagacattttgatgtcaattgttctgtttcaatatttaagctttgtactgttcttgattgccg-atgcttctattcatgct----

upper sequence: LOC_Os04g02820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G095851_T01 (Zea mays), 5'ss of exon 2
GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgctacaagatttgatctattaagactaacgatgttttacagtagtacttcttagttctagcagttagtgttgtatttcgcttttcctattgtat-
|  | |||||||||||||||||| | ||||||||| |||   || |||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||||| |   |   |    | ||  |    ||   |||  || |  ||    ||   ||   |   |  |   |   || || |||       |||    
GAAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGCGCTATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgttcagaacactgctctgtagcatatatatacatgcattgct-taacgttttcaagcctttttatgtgtagacttaatttgctccaatatttgagct

upper sequence: LOC_Os04g02820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S431_2V6.1 (Physcomitrella patens), 5'ss of exon 2
GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgctacaagatttgatctattaagactaacgatgttt--tacagtagtacttcttagttc-tagcagttagtgttgtatttcgcttttcctattgtat
            ||||||||  | | ||| ||||| ||    ||||||||||||||| | || ||||||||||||||||||||||| || || ||||| |||| ||   | ||  | | |  || |  || |  | ||| ||  ||   |   ||   | | ||| | | | | | | | | |  |  || |   |       
------------GTGAAGTTTTCAGCTGAGGAGCTCCGTGCTATTATGGACAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatcagaaactattacttagtg-gatttcctatgattactattctgacacaattgacttcatcgaattgaatttcgaaagttactctgtgttcaag--

upper sequence: LOC_Os04g02820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ28367 (Selaginella moellendorffii), 5'ss of exon 2
GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtg-ctacaagatttg--atctattaag--actaacgatgtttta-cagtagtacttcttagttctagcagttagtgttgtatttcgcttttcctattgtat
            ||||| |||||||  |||||||||||| |||| |||||||||||| | ||||| || ||||||||||| |||||||||||||| || |||  ||  || | ||||||   ||| ||| ||   |||| | |  |  | | | | |  |    ||                                        
------------GTGAAATTCACGGCAGAAGAGCTGCGCCGGATCATGGACAAGAAGCACAACATCCGGAACATGTCTGTGATTGCTCATGTCGATCACGgtgagtttcttctagattttccatccattcagtagctaaagctcgtcgatctgaaattttcgccag----------------------------------------

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|29680057|gb|CB676332.1|CB676332
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
EST: gi|58688395|gb|CK077082.1|CK077082
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
EST: gi|58661969|gb|CK050649.1|CK050649
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTTGCC
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATT-GCC
EST: gi|88718513|gb|CI742023.1|CI742023
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCANGCTTACAG
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAG
EST: gi|88395920|gb|CI593122.1|CI593122
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGGAAGCTGCTGGGATTATTGCCC
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
EST: gi|88372306|gb|CI619636.1|CI619636
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATT
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATT
EST: gi|88312172|gb|CI582510.1|CI582510
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGAT-CCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
EST: gi|29635546|gb|CB640555.1|CB640555
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
EST: gi|88740625|gb|CI764133.1|CI764133
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGG
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGG
EST: gi|88314758|gb|CI608217.1|CI608217
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTG
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTG
EST: gi|88388895|gb|CI592783.1|CI592783
EST:     CAAGAAGGATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTC-ACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTAT
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTAT
EST: gi|88363758|gb|CI609115.1|CI609115
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAG
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAG
EST: gi|702163|gb|D48454.1|D48454
EST:     CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATG                         GCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
genomic: CAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC
EST: gi|88403001|gb|CI568775.1|CI568775
EST:     ACCAAGAATAACATTCGTAACATGTCTGTCACTTGCTCATGTCGACCATG                         GCAAGTC-ACGCTTACAGATTCC-TTGTGGCAGCTGCTGGGATTATTGCCC
genomic: AG-AAGAATAACATTCGTAACATGTCTGTCA-TTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCC

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), 75 (downstream exon)
Score: 61

GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgcta ... ttccttgcagGCAAGTCCACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACCCGTGCAGATGAAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCAAGATGGTGAAGTTCACGGTTGAAGAGCTGCGCAGGATTATGGACAAGAAGAATAACATTCGTAACATGTCTGTCATTGCTCATGTCGACCATGgtatgtgctacaagatttgatctattaagactaacgatgttttacagtagtacttcttagttctagcagttagtgttgtatttcgcttttcctattgtat

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG