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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaaattagggtcaataataccatgattctgattctgccacccaattttcttatttctttattcttcctggaaaccctcctatttatgtttaatagactgaagattgcttttctttctaacgataatcag

Basic information

species Zea mays
transcript GRMZM2G000749_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000749_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 5'ss of exon 4
GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgt------gtaaattagggtcaataa-taccatgattctgattct-----gc-cacccaattttcttatttctttattcttcctggaaaccctcctatttatgtttaatagactgaagattg--cttttctttctaacgataatcag
||||||||||| || ||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||||||||||||||||| |       ||   ||     | ||| ||| |  | | |||||||     || |    ||||| | | |||||| ||||| | |  ||| |||| | || |||| | ||| ||||||  |||   ||| |||||||||   || |||
GTAATGCATGGGGCTGATCGTGATATTATGTGGCTCCAACGGGATTTCCACATATATGTTTGCAATCTTTTTGACACAGGACAGgtattttgattaataggctaataatactaaatactaaaactgtgattcttgattgcacctttaatttacctctttcttcattctccttcaaaatcctcattttcatgtcttataaactgaaccttggattttcctttctaactccaaacag

upper sequence: GRMZM2G000749_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G54440.2 (Arabidopsis thaliana), 5'ss of exon 4
GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaaattagggtcaataataccatgattctgattctgccacccaattttcttatttctttattcttcctggaaaccctcctatttatgtttaatagactgaagattgcttttctttctaacgataatcag
||||| ||||| || ||||| ||||| || ||||| || ||||||||   ||| ||||| |||||||||||||||||||||||||| ||    | ||  ||| | |       |  || |||    | ||    | ||     | | |    ||  | |   |   | | | ||  |  | |||  |  ||||| ||                       
GTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAGgtttg----atttctggttatt-------ttgttttgacatggtcatattacttggaggtgtatgagatcaccttaacagaacccattttggtagt-aatgta--gaagaatga----------------------

upper sequence: GRMZM2G000749_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaaattagggtcaataataccatgattctgattctgccacccaattttcttatttctttattcttcctggaaaccctcctatttatgtttaatagactgaagattgcttttctttctaacgataatcag
||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| ||||||||||||||||| ||  |   ||   | | || ||    |  || |   | || ||     | |      |     || |    |  | | | | |   || || || ||                                    
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcag-cgatgatcttctatttttttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg-----------------------------------

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|60338799|gb|DN205772.1|DN205772
EST:     TCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG                         GCTTCAAGGGTCTTACAGATGGAGAGAAACAGCCTTGAGCACCTATTGCTT
genomic: TCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaa ... cgataatcagGCTTCAAGGGTCTTACAGATGGAGAGAAACAGCCTTGAGCACCTATTGCTT




















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: 47 (upstream exon), 49 (downstream exon)
Score: 163

GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaa ... cgataatcagGCTTCAAGGGTCTTACAGATGGAGAGAAACAGCCTTGAGCACCTATTGCTTCATTTTTGTGGAGTAACAGCAAAGAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaa ... cgataatcagGCTTCAAGGGTCTTACAGATGGAGAGAAACAGCCTTGAGCACCTATTGCTTCATTTTTGTGGAGTAACAGCAAAGAAGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 224

GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaa ... cgataatcagGCTTCAAGGGTCTTACAGATGGAGAGAAACAGCCTTGAGCACCTATTGCTTCATTTTTGTGGAGTAACAGCAAAGAAGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 175

GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaa ... cgataatcagGCTTCAAGGGTCTTACAGATGGAGAGAAACAGCCTTGAGCACCTATTGCTTCATTTTTGTGGAGTAACAGCAAAGAAGGA