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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCCACATGCCGCCTATCTGCTCCCCGCTGGTTAGGCCAGGCCGACCCACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtttctctgttaacttcagctctttaattgaatggtgaatagataaatgaatgcagaatcgaatcctttccatagaagagggcatagttcatc...

Basic information

species Zea mays
transcript GRMZM5G886044_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G886044_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g20689.1 (Oryza sativa), 5'ss of exon 3
AGTTCCACATGCCGCCTATCTGCTCCCCGCTGGTTAGGCCAGGCCGACCCACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtttct--ctgttaacttcagctctttaattgaatggtgaatagataaatgaatgcagaatcgaatcctttccata-gaagagggcatagttcatc
|||||||||||||||||||||| |||||||| || || ||||| || ||  | || || || || ||||||||||||  ||| || ||| || | | ||||| | | ||  ||  |||||  || ||    |    |   |||     |   | ||||     |  || |  | ||||||||  | | |      | ||    
AGTTCCACATGCCGCCTATCTGTTCCCCGCTTGTCAGACCAGGACGGCCGGCAGAGGTGGCGCCAGTCATCTCCAAGAACCTAGAGGACATTCTCATGAGgtatatcgtgccttgctgttg-ctccattcgtcacgtaccatgtcctttgactgaatgggcatatcattg--tgctttccatgtgtataatctgcattttgct
















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|71432635|gb|DR813685.1|DR813685
EST:     ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAG                         TTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
genomic: ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtt ... ttttatgcagTTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
EST: gi|76011108|gb|DT938278.1|DT938278
EST:     ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAG                         TTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
genomic: ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtt ... ttttatgcagTTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
EST: gi|71438985|gb|DR820035.1|DR820035
EST:     ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAG                         TTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
genomic: ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtt ... ttttatgcagTTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
EST: gi|71427292|gb|DR808342.1|DR808342
EST:     ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAG                         TTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
genomic: ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtt ... ttttatgcagTTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
EST: gi|166617787|gb|EG215328.1|EG215328
EST:     GCTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAG                         TTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGG
genomic: ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtt ... ttttatgcagTTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGG
EST: gi|166622587|gb|EG229984.1|EG229984
EST:     GCTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAG                         TTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGG
genomic: ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtt ... ttttatgcagTTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGG
EST: gi|71438108|gb|DR819158.1|DR819158
EST:     ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAG                         TTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC
genomic: ACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtt ... ttttatgcagTTCTGGAATGCTAAATTTGAAGGACCTCTGTTTGATCACTGGGAAGGCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTCCACATGCCGCCTATCTGCTCCCCGCTGGTTAGGCCAGGCCGACCCACTGACGTTGCACCCGTCATCTCCAAGGCCCTTGAAGACGTTTTGACGAGgttttttgtttctctgttaacttcagctctttaattgaatggtgaatagataaatgaatgcagaatcgaatcctttccatagaagagggcatagttcatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA