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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctaccttcctgatattatggatatctgatcaggcttgtaattttgtaattttgattcttgttctgttgttttattggctccaaactgttacacat...

Basic information

species Oryza sativa
transcript LOC_Os02g13110.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 6
GTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctaccttcctgatattatggatatctgatcaggcttgtaattt--tgtaattttgat-tcttgttctgttgttttattggctccaaactgttacacat
|| || |||||||| || |  | |||  | ||| || | ||||||||| | ||||| ||||| |||||||||||||||||||||||||||||||||| | ||||| ||||||||||||||||| || |    || ||     | | || ||| | |     | |   ||||  ||| |||     | |   |   
GTTACAGGCCAAGAATTTACTCATGTTGCGAGAAGCAGACGTGTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttccttcatgatattatggatatctaataaaatctgcaaaacgatatgatcttgttgtacaaatgtccagtttccttgtctcattgttatctta---

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 6
GTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctaccttcctgatattatggatatctgatc-aggcttgtaattttgtaattttgattcttgttctgttgttttattggctccaaactgttacacat--------
|| ||  |||| ||    |   | ||  |  |||| ||  | |||||| | |||||||||||||| ||||||||||| ||||||||||| |||| |      ||    |  ||  || |  ||  |  |||||  | | | || ||| ||| || ||| |   |   |||||| | |  ||  |  |    ||        
GTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtga------tttgaaaccttgagggttcctattttaggctgttcagtgtggaatcttgctttttggt---tatctttatttgttttaacgtagtgttgatttgaaagt

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 6
GTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctaccttcctga----tattatggatatctgatcagg-------cttgtaattttgtaattttgattcttgttctgttgttttattggctccaaactgttacacat
|| ||  |||| ||    |   |  |  |  |||||||  | |||||| | |||||||||||||| ||||||||||| ||||||||||| |||| |  |     |  ||    |  |||     |||| ||||        ||||   ||| || || || |||  |  | | ||||  | |||  |  ||| |         
GTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtgatttgaaacctcgagggttcctataatagtctgttcagtgtcaaatcttgctttttggttatctttatttct--tttattgtagtgttgatttgaaagt---------

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 8
GTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctaccttcctgatattatggatatctgatcaggcttgtaattttgtaattttgattcttgttctgttgttttattggctccaaactgttacacat----
|| ||| |||| || | || || |||  | ||||| ||  | |||||| | |||||||||||||| ||||||||||| || |||||||| ||||  | ||    ||   |   ||  |  |    ||   |||   |     |  |||  |||  |   |      || | ||    |  ||| | |  | |    
GTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAGgtaggttattcacccattggaattcaacttgcttccttcttactagcaactgcttt--atttgtccgcaaaaaattcaatgatgtc--actataagtcgtctga

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 6
GTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctaccttcctgatattatggatatctgatcaggcttgtaattttgtaattttgattcttgttctgttgttttattggctccaaactgttacacat----
|| ||  |||| ||    ||||||||  | ||||||||  | || ||| | |||||||||||||||||||||||||| || || ||||  |||| |      ||||| |  ||       || | | |    | | | | |  |  | |  ||       | ||| | | ||    |  || | || ||  |    
GTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAGgt-aatcgttttcctaagttttc---cctcaggttatatgttttactcttgatatctctttaacacgtttttgctgtctttctccttaatttttccatctcagg

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|33675300|gb|CF303539.1|CF303539
EST:     GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG                         TGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
genomic: GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctacc ... ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
EST: gi|58688678|gb|CK077365.1|CK077365
EST:     GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG                         TGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
genomic: GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctacc ... ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
EST: gi|33675340|gb|CF303579.1|CF303579
EST:     GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG                         TGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
genomic: GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctacc ... ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
EST: gi|58681896|gb|CK070583.1|CK070583
EST:     GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG                         TGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
genomic: GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctacc ... ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
EST: gi|58663865|gb|CK052551.1|CK052551
EST:     GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG                         TGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
genomic: GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctacc ... ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
EST: gi|58680356|gb|CK069043.1|CK069043
EST:     GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG                         TGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA
genomic: GTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctacc ... ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAA

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: 62 (upstream exon), 56 (downstream exon)
Score: 36

GTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAGgttagctacc ... ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA




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