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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGTGAGCGTGTCGATGAGTATGGACTTGGTGTTAGAGAGAGCTTGGCTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttccacttctgttcctattcatcgtaattggccctacatcatttggtttttgagaaatttaaattcatttggtttttgagaaatttaaatgtcgctaaatccttgcgcatgtttggcag

Basic information

species Oryza sativa
transcript LOC_Os03g12590.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G012501_T02 (Zea mays), 5'ss of exon 15
AGAAAGTGAGCGTGTCGATGAGTATGGACTTGGTGTTAGAGAGAGCTTGGCTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttccacttct-gttcctattcatcgtaattggccctacatcatttggtttttgagaaatttaaattcatttggtttttgagaaatttaaatgtcgctaaatccttgcgcatgtttggcag
||| |||||||||||||||||||||||||| || |||||||| || |||||||||||||| | ||||||||||| ||||||||| |||||||| ||||||||||||||||| ||||   |   |   ||||| |    |||  |  |            |           ||||| ||| |||  |   | |||   | |                         
AGATAGTGAGCGTGTCGATGAGTATGGACTCGGGGTTAGAGAAAGTTTGGCTGAGGCTGTCAATGCTGTCATTAATATCCTTGGAATGCAGCCGTGTGAGgtcagtttccaattctcaatttcagaaatcgtcaaatccccccccccccccccacccccaccccccacgcatcattaggtatttctgggctataa-cattg-------------------------

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA06G01520.1 (Glycine max), 5'ss of exon 17
AGAAAGTGAGCGTGTCGATGAGTATGGACTTGGTGTTAGAGAGAGCTTGGCTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttccacttctgttcctattcatcgtaattggccctacatcatttggtttttgagaa-atttaaattcatttggtttttgagaaatttaaatgtcgctaaatccttgcgcatgtttggcag
 ||   |||||| || ||||||||||| ||||||  |||||||||||||||||| ||||| |   |||| || |   | |||||  || ||||||||||||| ||               ||  | |    |||||   ||     |  |  |||||||||  | || | || | |||  | |||    || |   |   |   ||   |||| ||          
TGATTTTGAGCGAGTGGATGAGTATGGTCTTGGTCCTAGAGAGAGCTTGGCTGAAGCTGTAAACACTGTTATCAACCTACTTGGCTTGGAGCCTTGTGAGgtaag---------------ctgatgaggtcaattgctgctttgataactcttttttgagaccactttatttaacttgtgtattgc---atgtgtgttgtgtacaacggttgcacaaa--------

upper sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 17
AGAAAGTGAGCGTGTCGATGAGTATGGACTTGGTGTTAGAGAGAGCTTGGCTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttccacttctgttcctattcatcgtaattggccctacatcatttggtttttgagaaatttaaattcatttggtttttgagaaatttaaatgtcgctaaatccttgcgcatgtttggcag
 ||   ||||||||| ||||||||||| ||||||  ||||||||| |||||||| ||||| | | |||| || |   | |||||  || ||||||||||||| ||         ||| |  | |  || |    |     |  || |  |   ||||||||    | | || ||||   || |            |  ||   ||   |||| ||          
TGATTTTGAGCGTGTGGATGAGTATGGTCTTGGTCCTAGAGAGAGTTTGGCTGAAGCTGTAAATACTGTTATCAACCTACTTGGCTTGGAGCCTTGTGAGgtaag---------ctgatgatgtcaattgctgct-----ttgataaactctcttttgaga----tcattttatttaacttgtatattgcacgtgttgcgtacaaaggttgcacaaag-------

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|58695561|gb|CK084248.1|CK084248
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|218498611|gb|FG960368.1|FG960368
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|86482482|gb|CI125115.1|CI125115
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|33656418|gb|CF279032.1|CF279032
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|88477306|gb|CI414577.1|CI414577
EST:     TGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: TGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|86513201|gb|CI155834.1|CI155834
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|14571493|gb|BI118861.1|BI118861
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACC
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACC
EST: gi|86478723|gb|CI121356.1|CI121356
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|22307514|gb|BQ908736.1|BQ908736
EST:     CTGTCATTAGTATCCTTGGTAT-CAGCCTTGTGAG                         GGCACTGAGGTTGTACCCAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|88482508|gb|CI419779.1|CI419779
EST:     GTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTTTCT
genomic: GTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|218500597|gb|FG956645.1|FG956645
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|88521041|gb|CI448695.1|CI448695
EST:     CTGAGGGTTTGAGTGCTTTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
EST: gi|86900021|gb|CI300117.1|CI300117
EST:     CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAG                         GGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT
genomic: CTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCT

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: 75 (upstream exon), 72 (downstream exon)
Score: 50

AGAAAGTGAGCGTGTCGATGAGTATGGACTTGGTGTTAGAGAGAGCTTGGCTGAGGCTGTGAGTGCTGTCATTAGTATCCTTGGTATGCAGCCTTGTGAGgtcagtttcc ... tgtttggcagGGCACTGAGGTTGTACCAAAGAATGCAAGATCGCACACTTGCCTGCTGTCTGGTGTGTTCATCGGCGACGCCAAGGTTCTTGTCAGGCTATCGTTTGGAC




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