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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctcaatattcttgagatctgcactcaatcgccacattcttttccgttatacttgttgaacaagttcacataatggatctctatttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGGGTACTGTACCCAATGCGAGGCCAACAGTTAATTACTCGTACTTGAGAAA

Basic information

species Zea mays
transcript GRMZM5G864414_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os06g02550.1 (Oryza sativa), 3'ss of exon 15
gtacctcaatattcttgagatctgca--ctcaatcgccacattcttttccgttatacttgttgaacaagttcacataatggatctctatttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGGGTACTGTACCCAATGCGAGGCCAACAGTTAATTACTCGTACTTGAGAAA
||   ||| ||| || | ||| |  |  |||| |     |||| ||       ||  || |||||  | ||   ||||| |||||          || |||||||||||||||||| |||||||||||   ||||||||| | | ||||  |  || | |||| ||| ||| | ||||||||||| ||||||||   
gtttgtcattatcctggcgatgtagaaactcatttttttcattattag--aacattgttattgaagcaatttgaataattgatct--------acagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGGGGCCCTTATCTAATGGGAGACCAGCCGTTAATTACTCATACTTGAGCGC
















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|32837059|gb|CD976737.1|CD976737
EST:     ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|20301126|gb|BQ164069.1|BQ164069
EST:     ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|111433841|gb|EE298127.1|EE298127
EST:     ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|71448844|gb|DR829894.1|DR829894
EST:     ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|60395565|gb|DN228435.1|DN228435
EST:     ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|32838225|gb|CD977903.1|CD977903
EST:     ACCTTCACTTCGCAAAAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|18963937|gb|BM660714.1|BM660714
EST:     ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|71417221|gb|DR803973.1|DR803973
EST:     ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: ACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
EST: gi|13558780|gb|BG550135.1|BG550135
EST:     TATGCATCAACGCCACCATCAG                         CTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG
genomic: TATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGG

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGGGTACTGTACCCAATGCGAGGCCAACAGTTAATTACTCGTACTTGAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 348

CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGGGTACTGTACCCAATGCGAGGCCAACAGTTAATTACTCGTACTTGAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 425

CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGGGTACTGTACCCAATGCGAGGCCAACAGTTAATTACTCGTACTTGAGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 287

CCATGCTTCTATGTCCCACCTTCACTTCGCTTCAAATCTACTGGATATGCATCAACGCCACCATCAGgtacctcaat ... atttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGGGTACTGTACCCAATGCGAGGCCAACAGTTAATTACTCGTACTTGAGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttccgttatacttgttgaacaagttcacataatggatctctatttctgtagCTGGGGCTAAAGGAGCTGTTGATCAGAAGAACATTAGGAGATACTACATGGGTACTGTACCCAATGCGAGGCCAACAGTTAATTACTCGTACTTGAGAAA
                                        tctctatttct  CT-rich tract
         ttatactt  TA-rich tract