Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagtacagattagcagtttatgttttgctacagataagttcagtttctgaaacttgacagtgacactccattcctttctgtgcag

Basic information

species Oryza sativa
transcript LOC_Os05g36270.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36270.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G322953_T04 (Zea mays), 5'ss of exon 2
GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagtac---agattagcagtttatgttttgctacagat---aagttcagtttctgaaacttgacagtgacactccattcctttctg--tgcag
|| |||||||| |||||||| || || || |||||||| |||||||| |||||||||||||||||||||||||| ||||  |  |     | | ||       ||       ||||  |   | ||||      |     |||||  || |||||    | ||  ||  |||||
GGCGAGGAGCAAAAGAAGCTGGATGTACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACCgtaacgcgctctcctacactacatacacatacacccgtacacgtcccaggttctcggcttaggcattgactttggcactctgcgctttcttgcgtgcag
















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|33679306|gb|CF307545.1|CF307545
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAG
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAG
EST: gi|88354625|gb|CI678668.1|CI678668
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|29670800|gb|CB667075.1|CB667075
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|29663073|gb|CB659348.1|CB659348
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|29644325|gb|CB649332.1|CB649332
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33684972|gb|CF313211.1|CF313211
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|88329945|gb|CI652332.1|CI652332
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33688486|gb|CF316725.1|CF316725
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33683625|gb|CF311864.1|CF311864
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|88309089|gb|CI654708.1|CI654708
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTC
EST: gi|29656833|gb|CB653108.1|CB653108
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|88332374|gb|CI656243.1|CI656243
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33688998|gb|CF317237.1|CF317237
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33686898|gb|CF315137.1|CF315137
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33693501|gb|CF321740.1|CF321740
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC

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), 50 (downstream exon)
Score: 45

GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCCCTCCGCGGAAA




<











<


<