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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgtcatttcttcttgcaattggtgtacctcctttaatcaatgttttgattctaagctgtttcaaatttgtacatgcaatttcttgcatggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGTGGTGGTGTTGGAGATGATGACTACATCTTTGCTTTTCAGACTGTGGTGC

Basic information

species Zea mays
transcript GRMZM2G107309_T07
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107309_T05 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g06980.1 (Oryza sativa), 3'ss of exon 11
ttgtgtcatttcttcttgcaattggtgtacctcctttaatcaatgttttgattctaagctgtttcaaatttgtacatgcaatttcttgcatgg-----atctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGTGGTGGTGTTGGAGATGATGACTACATCTTTGCTTTTCAGACTGTGGTGC
   || |  || || |   | ||  || ||||    |  |  |   ||   ||||||| || |||   ||| ||  || || |||||||||||     |  ||||||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||||||||  |||||||||| ||||||||| ||  ||||||||
-catgactctttttatcagagtttctg-acctagcatg-tggaaacttgagttctaagatgattcgt-tttatat-tgtaacttcttgcatgggcatcacttcagGTGGGAGTTATGGATGGCCAAGGATTCTCAGTCAATATACCTTGGAGCCGTGGTGGTGTTGGAGACAATGACTACATATTTGCTTTTAAGCATGTGGTGC
















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|60397976|gb|DN230792.1|DN230792
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|32930071|gb|CF034883.1|CF034883
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|211416077|gb|FK952655.1|FK952655
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|211416078|gb|FK952656.1|FK952656
EST:     CATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: CATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|32932636|gb|CF037448.1|CF037448
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAACTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|211416079|gb|FK952657.1|FK952657
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|9732030|gb|BE510782.1|BE510782
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGTATCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|211416082|gb|FK952660.1|FK952660
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
EST: gi|32834913|gb|CD974591.1|CD974591
EST:     ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAG                         GTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT
genomic: ATCGTCATGAGGATGGAAACTTTTACCCTGGAACTGGAGCTGCTCATGAGgtatctatct ... tggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgattctaagctgtttcaaatttgtacatgcaatttcttgcatggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGTGGTGGTGTTGGAGATGATGACTACATCTTTGCTTTTCAGACTGTGGTGC
 ttttgat  putative branch site (score: 4)
                tttcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgtcatttcttcttgcaattggtgtacctcctttaatcaatgttttgattctaagctgtttcaaatttgtacatgcaatttcttgcatggatctcagGTGGGAGTTCTTGATGGTCAAGGATTCTCAGTTAATATACCTTGGAGCCGTGGTGGTGTTGGAGATGATGACTACATCTTTGCTTTTCAGACTGTGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG