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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctgaacttctcgtaaccaactaaggtgacttgtttcgtattttccacctgtcccaaaacgttgagagatctgccgttttccatgcccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG

Basic information

species Zea mays
transcript GRMZM2G133959_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133959_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g72870.1 (Oryza sativa), 3'ss of exon 11
gtgagttctgaacttctcgtaaccaactaaggtgacttgtttcgtattttccacctgtcccaaaacgt-tgagagatctgccgttttccatgcccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
||||||||||| |||| |  | || ||||||  ||  ||| |  ||| || |  || ||  |||| || ||||| ||    | |||           |||||||| | || ||||| ||||| || |||||||||||||||||||||   |||
gtgagttctgagcttcac-catcccactaaga-gagatgtcttatatgtttctactatctgaaaatgtctgagacattactcctttatggcaaattgtgcagTACCATACGATGCGTAATGTTCTCTTCATGGCAATGACAGAGTTCACGAAG
















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|211416883|gb|FL440253.1|FL440253
EST:     CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGG                         TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
genomic: CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
EST: gi|71445212|gb|DR826262.1|DR826262
EST:     CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGG                         TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
genomic: CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
EST: gi|78080386|gb|DV508798.1|DV508798
EST:     CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGG                         TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
genomic: CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
EST: gi|76290046|gb|DV029614.1|DV029614
EST:     CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGG                         TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
genomic: CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
EST: gi|71431548|gb|DR812598.1|DR812598
EST:     CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGG                         TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG
genomic: CTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG

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: 37 (upstream exon), 49 (downstream exon)
Score: 11

GTCACTCCGACCTTCAATAACAAGGGGCATTGTGAGAAGGTTCCTTGGACCTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG


Block sizes: 41 (upstream exon), 41 (downstream exon)
Score: 11

GTCACTCCGACCTTCAATAACAAGGGGCATTGTGAGAAGGTTCCTTGGACCTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG


Block sizes: 38 (upstream exon), 42 (downstream exon)
Score: 21

GTCACTCCGACCTTCAATAACAAGGGGCATTGTGAGAAGGTTCCTTGGACCTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG


Block sizes: 44 (upstream exon), 41 (downstream exon)
Score: 11

GTCACTCCGACCTTCAATAACAAGGGGCATTGTGAGAAGGTTCCTTGGACCTTCATGGTCTGTAACAGCTGTTGATGCTGCATGCAGCCATCTCTTAAGGgtgagttctg ... cccattgcagTACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG