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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtctgcgtctctctctcgaccccaacagattactcccaaagcctcaatcgcaacactagcgacgacacactcactctagcgcttttgtttgcacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCGGCCGAGCTGGAGTCTCCATTTGCGTGACTGAAAAAGCTCCGCACTGCAC

Basic information

species Zea mays
transcript GRMZM2G116185_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116185_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g50900.1 (Oryza sativa), 3'ss of exon 4
gtaagcgtctgcgtctctctctcgaccccaacagattactcccaaagcctcaatcg----caacactagcgacgacacactcactctagcgcttt----tgtttgcacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCGGCCGAGCTGGAGTCTCCATTTGCGTGACTGAAAAAGCTCCGCACTGCAC
||||||  | || |||      | | |  | ||| |   |   ||  ||| ||| |       || || | || |   ||    | | |  |  |    | | |||   | ||||||||| ||||||||||| ||||||||| |||| || ||||||                                                          
gtaagctgcagcatcttctcacctatctaatcagttcggttaaaactcctaaattgatgcttgcaataacaacaattaacatgtttttgttccgtataatttctgctgattgcagCATCCAAGGACATGGGAAGCTCAGTTCCAGTCCGGTATCAAG----------------------------------------------------------
















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|20803186|gb|BQ294236.1|BQ294236
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|89250173|gb|DY621959.1|DY621959
EST:     GGAGCACGAAGATCAACCTCATCTCCTCCGGGAGCAACCCTGCCGACTCT                         CATCGGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCG
genomic: GGAGCACG-AGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCG
EST: gi|26456486|gb|CA828069.1|CA828069
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|50336651|gb|CO531777.1|CO531777
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCG
EST: gi|78112591|gb|DV530985.1|DV530985
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcaacactagcgacgacacactcactctagcgcttttgtttgcacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCGGCCGAGCTGGAGTCTCCATTTGCGTGACTGAAAAAGCTCCGCACTGCAC
                     cactcac  putative branch site (score: 2)
                                    ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgtctgcgtctctctctcgaccccaacagattactcccaaagcctcaatcgcaacactagcgacgacacactcactctagcgcttttgtttgcacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAGGTAGAGCCGGCCGAGCTGGAGTCTCCATTTGCGTGACTGAAAAAGCTCCGCACTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA