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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttctgtcacttagcacaagcatgttttttgcagtttgggttaatggatattctctatatctctgtagacacataaacacaatatttcattatg...

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 5'ss of exon 8
GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttctgtcacttagcacaagcatgtttt---ttgcagtt-tgggttaatggatattctctatatc-tctgtagacacataaacacaatatttcattatg
| || ||||| || ||||||||||||||||||||||| ||||||||| |  | | | |    |||||||  ||||    ||   || || ||||   | || |   |  ||  |     | |  | |   ||   ||   | ||  
GCTCATTTGGAACCGTGCACCGTGCGGATTGGAATGGCTCGgtatgtctctttttatt----acaagcacattttacagtgtgcttatgtgttacaagttactacttgaatagtgaccggtctaacatgtactgcatacaactac-
















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|32836824|gb|CD976502.1|CD976502
EST:     TACTGTGCACCGTGCGGATTGGAATGGTTCG                         GATGTGGCAGTAAAAATTCTAATGGAGCGGGACTTCCATCCAGAGCGTCTC
genomic: TACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
EST: gi|76284241|gb|DV023809.1|DV023809
EST:     GTTCTTTTGGTACTGTGCACCGTGCGGATTGAAATGGTTCG                         GATGTCGCAGNTAAAA-TTCTAATGGA
genomic: GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAG-TAAAAATTCTAATGGA
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GCGGATTGGAATGGTTCG                         GATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
genomic: GCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
EST: gi|32839244|gb|CD978925.1|CD978925
EST:     ACTGTGCACCGTGCGGATTGGAATGGTTCG                         GATGTGGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
genomic: ACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
EST: gi|32837172|gb|CD976850.1|CD976850
EST:     GGTACTGTGCACCGTGCGGATTGGAATGGTTCG                         GATGTGGCAGTAAAAATTCTAATGGAGCGGGACTTCCATCCAGAGCGTCTC
genomic: GGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
EST: gi|32838830|gb|CD978511.1|CD978511
EST:     TACTGTGCACCGTGCGGATTGGAATGGTTCG                         GATGTGGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
genomic: TACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
EST: gi|211082601|gb|FL182313.1|FL182313
EST:     GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG                         GATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTC
genomic: GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTC
EST: gi|32836743|gb|CD976421.1|CD976421
EST:     ACTGTGCACCGTGCGGATTGGAATGGTTCG                         GATGTGGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC
genomic: ACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTC

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: 40 (upstream exon), 49 (downstream exon)
Score: 71

GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTCAAAGAATTTTTGAGAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTCAAAGAATTTTTGAGAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 67

GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTCAAAGAATTTTTGAGAGAG


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 32

GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCGgtatgttttc ... tttaacccagGATGTCGCAGTAAAAATTCTAATGGAGCAGGACTTCCATCCAGAGCGTCTCAAAGAATTTTTGAGAGAG