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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttctgaattgatatactcaacacattatatgtttttccattcgatgataaaataattatctaagctaaacttatccagctctagTGAAGCAAGATTTCCAATTCCTGATATAATCCTAAGAACAGTTACTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG

Basic information

species Zea mays
transcript GRMZM2G177575_T01
intron # 6
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|148971473|gb|EE022167.2|EE022167
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAGCTCTAG                    
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTT--G----AGgttattttct ... ccagc
EST: gi|149106837|gb|EE188735.2|EE188735
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAGCTCTAG                    
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTT--G----AGgttattttct ... ccagc
EST: gi|86469449|gb|DY235819.1|DY235819
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAGCTCTAG                    
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTT--G----AGgttattttct ... ccagc
EST: gi|78110126|gb|DV528541.1|DV528541
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAG                         C
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAGgttattttct ... ccagctctag-
EST: gi|78110126|gb|DV528541.1|DV528541
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAG                         C
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAGgttattttct ... ccagctctag-
EST: gi|78086094|gb|DV514487.1|DV514487
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAGCTCTAG                    
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTT--G----AGgttattttct ... ccagc
EST: gi|76293066|gb|DV032634.1|DV032634
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTGGAATATTGTTATGATTTGAGCTCTAG                    
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTT--G----AGgttattttct ... ccagc
EST: gi|213178693|gb|FM194771.1|FM194771
EST:     CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTTGAGCTCTAG                    
genomic: CGTCATGCTGCTGACTCCAGGATTCCTTTTGAATATTGTTATGATTT--G----AGgttattttct ... ccagc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttccattcgatgataaaataattatctaagctaaacttatccagctctagTGAAGCAAGATTTCCAATTCCTGATATAATCCTAAGAACAGTTACTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG
                                 agctaaa  putative branch site (score: 3)
                                        cttatcc  CT-rich tract
                 ataaaataattatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattttctgaattgatatactcaacacattatatgtttttccattcgatgataaaataattatctaagctaaacttatccagctctagTGAAGCAAGATTTCCAATTCCTGATATAATCCTAAGAACAGTTACTGGAAGTATGTTTCCTGTTATTGATCCAGGGCAAGTAATCTCCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG