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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctatacatgctgatccaccagccttaccctattagcttgaatttcttctgtttttacgcacggttcctttgattgtattcgatctaccattaccatgcatgaggagatcattattattttgtagataaaaatattctctgtgcag

Basic information

species Zea mays
transcript GRMZM5G881387_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G881387_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g48229.1 (Oryza sativa), 5'ss of exon 1
AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctatacatgctgatccaccagccttaccctattagcttgaatttcttctgtttttacgcacggttcctttgattgtattcgatctaccattaccat-gcatgaggagatcattattattttgtagataaaaatattctctgtgcag
|||||| ||   || ||||||||| |||||| ||||| || ||||||||||||||||| | |||||||||| ||| ||||||| ||||||||||||||||||   ||      |  ||||  |   |    | ||  ||   |    |||  | | || ||  |   | ||  |||          ||   |   | |  || ||||                                             
AAGGCCAACAAGAAGGCCTGCAGGTCCTTCGACGACTTCGACCTCTCCTTCAAGCCCAAGCCCGGCGGCCTCCCCATCTTCCTCCTCGTCGATCGCGGAGgtcc-tccccctttcttgatttattcg----aacccgtt---tcagtttttatttattattgggggagatttattttccctctcgtgagtgattttaaatatcgcatc--------------------------------------------
















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|149080543|gb|EE169581.2|EE169581
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|148941690|gb|EC886638.2|EC886638
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCT
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCT
EST: gi|148962771|gb|EE013682.2|EE013682
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|148982822|gb|EE028662.2|EE028662
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|149062894|gb|EE157615.2|EE157615
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|148953630|gb|EC898987.2|EC898987
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|149009841|gb|EE041718.2|EE041718
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAG
EST: gi|211192275|gb|FL063588.1|FL063588
EST:     CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAG                         ATTGCTACTTCACAACCA
genomic: CAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCA

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 3 RNA-Seq libraries.


Block sizes: 35 (upstream exon), 24 (downstream exon)
Score: 5

AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC


Block sizes: 25 (upstream exon), 34 (downstream exon)
Score: 3

AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 367

AAGGCCGACGCCAAAGCCTGCAGGCCCTTCGCCGACTCCGGCCTCTCCTTCAAGCCCAGGTCCGGCGGCCTGCCCGTCTTCCTGCTCGTCGATCGCGGAGgtatatctat ... ctctgtgcagATTGCTACTTCACAACCAAGGGATGGAACGCACAGAACGCCGGAGCTGCAGCAGTTCTTGTGGCCGACGACAGAGTGGAGCCTCTGATCACGATGGACTC