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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctggaaattgatgtatgacagtaaattttttatgttggaactgtttacatgtatgttccttgaaatttatcttttatctcaccatttgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGCAACAGCAACTTCTGTGATCTTCAAAAAGAATGCTCCACAGCATTGCAAT

Basic information

species Zea mays
transcript GRMZM2G177575_T01
intron # 2
splice site 3'
intron type U2

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|91875997|gb|EB405954.1|EB405954
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         GCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
EST: gi|88757255|gb|DY541396.1|DY541396
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         GCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
EST: gi|148934199|gb|EC878220.2|EC878220
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         GCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
EST: gi|78086095|gb|DV514488.1|DV514488
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         GCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
EST: gi|211464476|gb|FK971163.1|FK971163
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         GCTACATTTTACATCCCTG
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCCCTG
EST: gi|211461959|gb|FK971158.1|FK971158
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGGCTCTGGATCA                         GCTACATTTTACATCC
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCC
EST: gi|148971474|gb|EE022168.2|EE022168
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         T
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcag-
EST: gi|148971474|gb|EE022168.2|EE022168
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         T
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcag-
EST: gi|148971474|gb|EE022168.2|EE022168
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         T
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcag-
EST: gi|148971474|gb|EE022168.2|EE022168
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         T
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcag-
EST: gi|148971474|gb|EE022168.2|EE022168
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         T
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcag-
EST: gi|148971474|gb|EE022168.2|EE022168
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         T
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcag-
EST: gi|149005051|gb|EE039576.2|EE039576
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         GCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
EST: gi|149079839|gb|EE168839.2|EE168839
EST:     CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCA                         GCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC
genomic: CTTGCCAGTGTGACGGCTGCACGCCTCCAGCCACTGCTGCCTCTGGATCAgtaagagctc ... tgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttacatgtatgttccttgaaatttatcttttatctcaccatttgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGCAACAGCAACTTCTGTGATCTTCAAAAAGAATGCTCCACAGCATTGCAAT
                                  atctcac  putative branch site (score: 3)
                  ttgaaatttatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctggaaattgatgtatgacagtaaattttttatgttggaactgtttacatgtatgttccttgaaatttatcttttatctcaccatttgagtttcagGCTACATTTTACATCCCTGGTATGTCGTCAACTAGTAAAGCAGTTCCGTGCAACAGCAACTTCTGTGATCTTCAAAAAGAATGCTCCACAGCATTGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - atgtatg
- - - - - - - - - - - - - - - - - tatgttg
- - - - - - - - - - - - - - - - - - - - - -actgttt