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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctattttctgttattactgcatatatatttgcctttgtatgtggttgttttgacgtgccgcttactgtgctttag

Basic information

species Zea mays
transcript GRMZM2G314679_T06
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G314679_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 5'ss of exon 4
ATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctattttctgttattactgcatatatatttgc-ctttgt--atgt------ggttgttt--tgacgtgccgcttactgtgctttag
| |||||||| ||||||||||||||||| ||||||||||||||||||||  |||||| ||||||||| || || |||||||||||||||||| |||||||||  | || ||  |   | || | || ||  | |||   |||||  ||||      || |||||  | |    | ||||||||||||||||
AAGACCTTCATTTTTTTGTCACCGCTGGTGATGATGAGAATGAGCTCATTATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtacttctt-ccagtattccacatgaacttgtattttgttaatgttggtaaggctgtttctttaaagtcagcttactgtgctttag
















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|211411155|gb|FK961654.1|FK961654
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|60356728|gb|DN223701.1|DN223701
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|32849532|gb|CD989213.1|CD989213
EST:     ACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: ACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|15323565|gb|BI478787.1|BI478787
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|4681229|gb|AI629899.1|AI629899
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|32908218|gb|CF013031.1|CF013031
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|32938645|gb|CF043464.1|CF043464
EST:     ACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: ACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|4646698|gb|AI491558.2|AI491558
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGTCTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|5296305|gb|AI783075.1|AI783075
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|91873753|gb|EB403710.1|EB403710
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|5901227|gb|AW042327.1|AW042327
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|16925380|gb|BM078448.1|BM078448
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCT
EST: gi|6227104|gb|AW155808.1|AW155808
EST:     TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAG                         GNGGTGATGTTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTT
genomic: TTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctatt ... tgtgctttagG-GGTGATGTT-GAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTTAGCAAGTGTACTACATGGTTTTTCTGATTCTGTTGGTCTTCTACTCAGgttgtctattttctgttattactgcatatatatttgcctttgtatgtggttgttttgacgtgccgcttactgtgctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG