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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCTCGCGCCCGCTCGAGGACGCCGTCGCGGATTTCCTCGCACGCGTGCCCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggctttttgtgaccagagaccctcccggccgcttatgtctagtttcagtcgccgcgtttcgttggattgctgggttttcaggtttttaggggtg...

Basic information

species Zea mays
transcript GRMZM2G011575_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011575_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 5'ss of exon 1
CGTCTCGCGCCCGCTCGAGGACGCCGTCGCGGATTTCCTCGCACGCGTGCCCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggctttttgtgaccagagaccctcccggccgcttatgtctagtttcagtcgccgcgtttcgttggattgctgggttttcaggtttttaggggtg
|||   ||||||||||||||||| ||| ||||| |||||||| ||| | |  ||||| ||||||||||| |||||| || |||| | |||||||||| ||||     ||   |          ||  | |||   ||||   | |      |     | || |   |     | | | |        |       || | 
CGTGAAGCGCCCGCTCGAGGACGTCGTGGCGGACTTCCTCGCCCGCATCCAGCCCGAGCGCCGCCTCCGCTTCGGCGCCGCCATAAACTTCGTCCTCAAGgtaacccgcccctccctggattggattccccccctcgctcccgcccgcccgcgtcgtctgcttgatgcctcctggttcgaggcgagcgcccgctcggctt
















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|91048056|gb|EB158474.1|EB158474
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|71307834|gb|DR790138.1|DR790138
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|211502396|gb|FK960896.1|FK960896
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|29167999|gb|CB411259.1|CB411259
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTTCTTTTT                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|31358140|gb|CD442497.1|CD442497
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|211502392|gb|FK960892.1|FK960892
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
EST: gi|148933022|gb|EE285909.2|EE285909
EST:     CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAG                         GACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA
genomic: CCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggct ... ctctaatcagGACAAGATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCTCGCGCCCGCTCGAGGACGCCGTCGCGGATTTCCTCGCACGCGTGCCCCCCGATCGCCGCCTCCGGTTCGGCACCTCCATCAGCTTCGTCCTCGAGgtgcgtggctttttgtgaccagagaccctcccggccgcttatgtctagtttcagtcgccgcgtttcgttggattgctgggttttcaggtttttaggggtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc