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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttccccctattttgggtttatctttgttttgttgtgaaacttcaaattcttcattgtttcaattctattttgttgcttggtgcag

Basic information

species Zea mays
transcript GRMZM2G037200_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037200_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g45480.4 (Oryza sativa), 5'ss of exon 2
TTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttccccctattttgggtttatctttgttttgttgtgaaacttcaaattcttcattgtttcaattctattttgttgcttggtgcag
||||||||||||||||  ||||||||||| ||||||||| ||||| |||||||||||||||||||| ||||  | |||| |||||||||| ||||||||||||| ||||     |  ||   |||   |  |||| ||  | | | ||  | || |  | |  |||| |  |  |      ||||||||||
TTGGAATATGCAAACACAAGCGGAAATGAACCTTACTGGGCCAACGGGGCAAGTCTATGCACTCGCTGTTGGAAATGAGCTACTCTTTGCCGCAACACAAgtaaacttc-----acattcattttgcttacgtttggtcctaacattttta-ttgtcgaatcattcactcgtgatgcc---cttggtgcag
















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|29576800|gb|CB616912.1|CB616912
EST:     AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
genomic: AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
EST: gi|31997696|gb|CD661719.1|CD661719
EST:     AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
genomic: AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
EST: gi|26559549|gb|CA831784.1|CA831784
EST:     AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
genomic: AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
EST: gi|95107946|gb|EB740175.1|EB740175
EST:     AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
genomic: AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
EST: gi|22715752|gb|BU197942.1|BU197942
EST:     AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
genomic: AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
EST: gi|22819542|gb|BU499632.1|BU499632
EST:     AGGCTATGCACTCCGCGGT-GCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTT
genomic: AGTCTATGCACTC-GCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTT
EST: gi|29576814|gb|CB616926.1|CB616926
EST:     AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
genomic: AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
EST: gi|87157418|gb|DY402207.1|DY402207
EST:     AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAA                         GCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG
genomic: AAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttcc ... cttggtgcagGCTGGGAGGATTTTAGCATGGAGATTTAGTGCCGCAACTAACTGTTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACACAAgtaagcttccccctattttgggtttatctttgttttgttgtgaaacttcaaattcttcattgtttcaattctattttgttgcttggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC