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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACTTTGCGTCGGAGGTCCACTCCGGCAATCTGAAGAATTTCGGTCTCATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttctccatccttttttttcgtcaccatgagcgggctaacgttggcaactgttctcgtattcagcgtttcccttgttttcctgaatcactgtgtttgtttaccag

Basic information

species Zea mays
transcript GRMZM2G086934_T01
intron # 2
splice site 5'
intron type U2

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|148943263|gb|EC888324.2|EC888324
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|211530807|gb|FL076080.1|FL076080
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGACGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|50331879|gb|CO527005.1|CO527005
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|211527807|gb|FL076066.1|FL076066
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCG
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCG
EST: gi|78024319|gb|DV492706.1|DV492706
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|148976840|gb|EE025967.2|EE025967
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|78081808|gb|DV510220.1|DV510220
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|78024998|gb|DV493385.1|DV493385
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|5566971|gb|AI881882.1|AI881882
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGTGACTGTGTGCGAAGCGCTCGACGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
EST: gi|149086433|gb|EE175976.2|EE175976
EST:     ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAA                         AGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA
genomic: ATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 754

CTTACTTTGCGTCGGAGGTCCACTCCGGCAATCTGAAGAATTTCGGTCTCATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGAGATCAACGGCGAGGCCAAGAAAGAGGATCCTCCAATTGTGCTGAAGCCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 146

CTTACTTTGCGTCGGAGGTCCACTCCGGCAATCTGAAGAATTTCGGTCTCATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGAGATCAACGGCGAGGCCAAGAAAGAGGATCCTCCAATTGTGCTGAAGCCT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 129

CTTACTTTGCGTCGGAGGTCCACTCCGGCAATCTGAAGAATTTCGGTCTCATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGAGATCAACGGCGAGGCCAAGAAAGAGGATCCTCCAATTGTGCTGAAGCCT


Block sizes: 45 (upstream exon), 41 (downstream exon)
Score: 36

CTTACTTTGCGTCGGAGGTCCACTCCGGCAATCTGAAGAATTTCGGTCTCATCCGCATCCTCGACTACACTTGCAACTCCGTCAAAGGCAACGCTGACAAgtaagtgttc ... tgtttaccagAGTCCTGATTGTCGTCAAATGCGAGACTGTGTGCGAAGCGCTCGATGCCGAGATCAACGGCGAGGCCAAGAAAGAGGATCCTCCAATTGTGCTGAAGCCT