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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTACCGATAACTATATCATTCTCCTCGCACTTGTGTACTGCGTAACCGGTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatcataaagattgttcaacttttgcagtttcttctgattaataatatatttggagactaaccctgaaacttttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g11820.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g11820.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G455476_T01 (Zea mays), 5'ss of exon 8
AATTACCGATAACTATATCATTCTCCTCGCACTTGTGTACTGCGTAACCGGTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatcataaagattgttcaacttttgcagtttcttctgattaata-----atatatttggagactaaccctgaaactt-ttgcag
|||| | |||||||| ||  | |||||||| ||||||||||| || || || ||||||||||||||||| ||||||||||  ||||| || ||||| |||||| ||||||| |  |||  |    |  | |    ||| |||| | ||      | ||||    |  || |  | ||  ||| |  |||
AATTGCTGATAACTACATTGTGCTCCTCGCGCTTGTGTACTGTGTGACTGGGATAGGATACACTTTTGCCATCTGCTTCAGTCCTGGCTCAGCACAGCTGgtaggtatcatgacaattaattttttcgtacgacatctcctgaatgattggcccacatatacttaacctcattccgatgcttgtcacag
















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|88255823|gb|CI353694.1|CI353694
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
EST: gi|88234008|gb|CI233857.1|CI233857
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
EST: gi|88233917|gb|CI233766.1|CI233766
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
EST: gi|89194779|gb|CI003243.1|CI003243
EST:     TATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACCTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAA
genomic: TATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAA-CTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAA
EST: gi|88235761|gb|CI234963.1|CI234963
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
EST: gi|29672932|gb|CB669207.1|CB669207
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
EST: gi|86842427|gb|CI335307.1|CI335307
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTCTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
EST: gi|88233937|gb|CI233786.1|CI233786
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
EST: gi|86480263|gb|CI122896.1|CI122896
EST:     GTATAGGATACACTTTTGCTATCTGCTTCAACTCTGGTTCTGCACAACTG                         TGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT
genomic: GTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAAT

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: 20 (upstream exon), 56 (downstream exon)
Score: 1

AATTACCGATAACTATATCATTCTCCTCGCACTTGTGTACTGCGTAACCGGTATAGGATACACTTTTGCTATCTGCTTCAACCCTGGTTCTGCACAACTGgtatgtatca ... acttttgcagTGTTCTGCATTGATCCCAGTTGTTCTGACTTTGTTATCCACTCAAAATAATACCCCTGCAATTCTCAATAGATTATGCTATCCAAAGTGGGCATTAGAGG




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