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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccattagtaactttatgcattactatgcctagtgtatgccttgttatgttgtggagcggagcagtcatcaccatcaattttgctgctgttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCAG

Basic information

species Oryza sativa
transcript LOC_Os07g49270.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 12
--tcccattagtaactttatgcattactatgcctagtgtatgcc--ttgttatgttgtggagcggagcagtcatcaccatcaat-tttgctgctgttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCAG
         | ||  | ||||    |||       ||   | ||   || ||| |  |  |       || ||| |    ||   ||| |   | ||| |||||||| |||||| ||||||| |||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||
gtaagtggaaatacttgtatgttccactgaatggggttgtttccaactgatatttgttatattttgttaggcattatttgcatcattttcctttatttacttcagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGCCCAACAAAACACATGCCAACACCTGAGCAATGGACTAATATTTTCAATCCAG
















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|58694980|gb|CK083667.1|CK083667
EST:     TTCACAT-CTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|86871926|gb|CI332098.1|CI332098
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|86599171|gb|CI355788.1|CI355788
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|29671780|gb|CB668055.1|CB668055
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|88276104|gb|CI396708.1|CI396708
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|29663749|gb|CB660024.1|CB660024
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|88901869|gb|CI374477.1|CI374477
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|58686177|gb|CK074864.1|CK074864
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAA
EST: gi|33793650|gb|CF322709.1|CF322709
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|88265236|gb|CI369010.1|CI369010
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGAGTTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCC
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGA-TTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCC
EST: gi|88906500|gb|CI375572.1|CI375572
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|86602782|gb|CI357146.1|CI357146
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|88970069|gb|CI383571.1|CI383571
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|88263167|gb|CI366941.1|CI366941
EST:     TAACTGTTGATCATGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|88835899|gb|CI371004.1|CI371004
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATTTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|88839179|gb|CI378103.1|CI378103
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|89196317|gb|CI397319.1|CI397319
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|86889206|gb|CI315817.1|CI315817
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         TTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
EST: gi|86883261|gb|CI328682.1|CI328682
EST:     TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAG                         GTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA
genomic: TAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCA

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: 72 (upstream exon), 75 (downstream exon)
Score: 27

CAATTCTTTCCAGAACCTCCTTGACAATATTTTTCTGCCTCTTTTTGAAGTAACTGTTGATCCTGCTTCACATCCTCAGCTCCATGTTTTCTTGCAACAGgtcagtggaa ... ttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgttgtggagcggagcagtcatcaccatcaattttgctgctgttttcttcagGTCGTTGGGCTGGATTTAGTGGATGATGAAAGCAAACCAGAGAGACGCCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCAG
                                       ctgctgttttcttc  CT-rich tract
                             atcaatttt  TA-rich tract