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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGTACTATCTCCTCCGCAAGTGCGGCGGCCTGCCGCTCGCCGCGCCGGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcag

Basic information

species Zea mays
transcript GRMZM2G123667_T05
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123667_T05 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 5'ss of exon 1
GTGATGTACTATCTCCTCCGCAAGTGCGGCGGCCTGCCGCTCGCCGCGCCGGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcag
||||||||||| ||   |||||||||||||||||| || |||||||| ||||| |||||||||||||| |||||||||||| |||||||| | ||||| |||| |    |  |   |   ||||  | ||| |          ||||  |  |    | |||   |    | |  | ||  |  |   |||       | |||||||
GTGATGTACTACCTGTGCCGCAAGTGCGGCGGCCTCCCCCTCGCCGCCCCGGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaagagcaaaagcagatcga-atcgaat----------cgaggaaattgaa-gtcgaattcaaattcaattaattggg-gatttgg-----aattgttgcag

upper sequence: GRMZM2G123667_T05 (Zea mays), 5'ss of exon 1
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 5'ss of exon 1
GTGATGTACTATCTCCTCCGCAAGTGCGGCGGCCTGCCGCTCGCCGCGCCGGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcgctgacctcatcagctggcat-ggtgatcggtggttgcag
||| || | |||||  | || || ||||     | |    || |||  ||| | || |||||||| ||||||||||||| ||| ||||||||||| |||||||  |     | ||   |  |  ||      | | || | |   | |       ||||  |  ||    |||  | || |   |   | | |  || |   | |   
GTGGTGCATTATCTGGTTCGTAAATGCGCATCACAGAGCATCTCCGTTCCGATTATTGCCGAGGTTGATCTCTACAAGTACGATCCATGGCAGCTTCCAGgtattttttttattctctt--ttctctttctttttcagatttggaaaccttaagtgtgagaaatcc----tgatttgatgattcgaattcgattctctgaaatggg--
















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|211322211|gb|FL322860.1|FL322860
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|38687829|gb|CK144860.1|CK144860
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211075262|gb|FL326781.1|FL326781
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211331126|gb|FL341576.1|FL341576
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211518019|gb|FL144160.1|FL144160
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211165931|gb|FL144172.1|FL144172
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211165934|gb|FL144175.1|FL144175
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGAGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|17921555|gb|BM259206.1|BM259206
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211165936|gb|FL144177.1|FL144177
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|17921883|gb|BM259534.1|BM259534
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211145460|gb|FL359539.1|FL359539
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAAGAAGGAGTGGTACTTCTTCTCGCCGCGCGAC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGA-GAAGGAGTGGTACTTCTTCTCGCCGCGCGAC
EST: gi|211449319|gb|FL365458.1|FL365458
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211518024|gb|FL144165.1|FL144165
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211329589|gb|FL022638.1|FL022638
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|19351281|gb|BM895813.1|BM895813
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211127219|gb|FL366470.1|FL366470
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211165928|gb|FL144169.1|FL144169
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAAAAAAGGAGTGGTACTTCTTCTCGCCGCGCGA
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAA--GGAGTGGTACTTCTTCTCGCCGCGCGA
EST: gi|89756736|gb|DY686654.1|DY686654
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|211285411|gb|FL349550.1|FL349550
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
EST: gi|88756318|gb|DY540459.1|DY540459
EST:     GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAG                         AGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC
genomic: GGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaa ... gtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGTACTATCTCCTCCGCAAGTGCGGCGGCCTGCCGCTCGCCGCGCCGGTCATCGCCGAGGTGGATCTCTACAAGTTCGACCCATGGCAGCTCCCAGgtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC