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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaaatgtctttgccggacaaatttcaccaatctggctacgaatgatgcttgatcacttcttttgttttatctaaaagttccatgtcttatgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTGAAGTTGATGCACATGGTGTGGACCAAGAGCTGAAGCACCATCTCCTGAA

Basic information

species Zea mays
transcript GRMZM2G017087_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017087_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g51690.3 (Oryza sativa), 3'ss of exon 2
--agtaaatgtctttgccggacaaatttca-ccaatctggctacgaatgatgcttgatcacttcttttgttttatctaaaagttccatgtcttatgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTGAAGTTGATGCACATGGTGTGGACCAAGAGCTGAAGCACCATCTCCTGAA
    || | || ||| | |      ||| |   | |||  ||| |  |||  | | |||| || | |||| ||  ||||   || | |||   ||| |||||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||  ||||||||||||||||||| || ||||| ||||||||| | |||||
gatctacacgtttttcctgatttcttttgaattagtctacctatg--tgaaccataatcaatt-tcttgtctttgctaactatttcgtgtgacatgtttgaagGCTCTTCTGAGGAGGACCAAGAAGGTAGCGGAGGAGAGACAGAGCTACCTGAGATTGATGCACATGGTGTGGATCAGGAGCTCAAGCACCATTTGCTGAA
















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|86469581|gb|DY235951.1|DY235951
EST:     GCGCAACATCCTTTCATTTG                         GCTCTTTTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: GCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|211385201|gb|FK954733.1|FK954733
EST:     GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTWGCGGAGGAGAGACCGAGCTCCCTG
genomic: GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|22542334|gb|BU092787.1|BU092787
EST:     GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|211382575|gb|FK954728.1|FK954728
EST:     GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|74236767|gb|DT644681.1|DT644681
EST:     TCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: TCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|21987869|gb|BQ779397.1|BQ779397
EST:     GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|76019795|gb|DT946965.1|DT946965
EST:     GAACTCGCTTTCCATTTCCGGAAGGTCGGTGGGCAACATCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|211385208|gb|FK954740.1|FK954740
EST:     GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
EST: gi|60357235|gb|DN224208.1|DN224208
EST:     GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTG                         GCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG
genomic: GAACTCGCTTTCCATCTCCGGAAGGTCGCTGCGCAACATCCTTTCATCTGgtactgaagt ... atgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcttgatcacttcttttgttttatctaaaagttccatgtcttatgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTGAAGTTGATGCACATGGTGTGGACCAAGAGCTGAAGCACCATCTCCTGAA
                         atctaaa  putative branch site (score: 3)
                ttttgttttatctaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaaatgtctttgccggacaaatttcaccaatctggctacgaatgatgcttgatcacttcttttgttttatctaaaagttccatgtcttatgcttgaagGCTCTTCTGAGGAGGATCAAGAAGGTAGCGGAGGAGAGACCGAGCTCCCTGAAGTTGATGCACATGGTGTGGACCAAGAGCTGAAGCACCATCTCCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC