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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTCTGATGTGGTGATTGTTGAGGCAAAAGAAGGCAAACCTATTCGAATAAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAAgtaattcgtgaaccttcaaatataacagatacatattttaatctcaatatcaaatttgttgtcttagtttactgcatattttcag

Basic information

species Zea mays
transcript GRMZM2G042253_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042253_T01 (Zea mays), 5'ss of exon 12
lower sequence: 13114.m00140 (Oryza sativa), 5'ss of exon 12
ACCTCTGATGTGGTGATTGTTGAGGCAAAAGAAGGCAAACCTATTCGAATAAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAAgtaattcgtgaaccttcaaatataacagatacatattttaatctcaatatcaaatttgttgtcttagtttactgcatatttt-cag
|| ||||| ||||||||||||||||| ||||||||||||||  |||| ||||| ||||| ||||||||||     || || |||||||||||||||||  |||| |     ||||||| |||  |||   |  | | |  |    ||||||   ||  |||  | | ||| |||| | |||| |||
ACATCTGACGTGGTGATTGTTGAGGCGAAAGAAGGCAAACCAGTTCGCATAAGGCCCCCGATGCCTCCTAAAAGTTTGATACCCCCAATGCCTGCTTCTGgtaactaccacaccttcatataggaca--caagtttctccactggaatatc---ttgcttgcttaactttgctgcttgtttttcag
















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|16380029|gb|BI993272.1|BI993272
EST:     AAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAA                         TTTCAGGTATTCGAGTGTAGCAGGCGTCCTTTCCACCAAGAATCAGCCTCA
genomic: AAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAAgtaattcgtg ... atattttcagTTTCAGGTATTCGAGTGTAGCAGGCGTCCTTTCCACCAAGAATCAGCCTCA
EST: gi|211281517|gb|FL449052.1|FL449052
EST:     AAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAA                         TTTCAGGTATTCGAGTGTAGCAGGCGTCCTTTCCACCAAGAATCAGCCTCA
genomic: AAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAAgtaattcgtg ... atattttcagTTTCAGGTATTCGAGTGTAGCAGGCGTCCTTTCCACCAAGAATCAGCCTCA

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: 46 (upstream exon), 49 (downstream exon)
Score: 26

ACCTCTGATGTGGTGATTGTTGAGGCAAAAGAAGGCAAACCTATTCGAATAAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAAgtaattcgtg ... atattttcagTTTCAGGTATTCGAGTGTAGCAGGCGTCCTTTCCACCAAGAATCAGCCTCAACACAACAAGACTACGGGCCCGGTACCCCCAAGTTTCTAAGATAATAAA


Block sizes: 39 (upstream exon), 11 (downstream exon)
Score: 1

ACCTCTGATGTGGTGATTGTTGAGGCAAAAGAAGGCAAACCTATTCGAATAAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAAgtaattcgtg ... atattttcagTTTCAGGTATTCGAGTGTAGCAGGCGTCCTTTCCACCAAGAATCAGCCTCAACACAACAAGACTACGGGCCCGGTACCCCCAAGTTTCTAAGATAATAAA


Block sizes: 45 (upstream exon), 38 (downstream exon)
Score: 5

ACCTCTGATGTGGTGATTGTTGAGGCAAAAGAAGGCAAACCTATTCGAATAAGACCCCCAATGCCTCCTAGGCACTTAATTCCCCCAATGCCTGCTTCAAgtaattcgtg ... atattttcagTTTCAGGTATTCGAGTGTAGCAGGCGTCCTTTCCACCAAGAATCAGCCTCAACACAACAAGACTACGGGCCCGGTACCCCCAAGTTTCTAAGATAATAAA