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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggggacatgatgtccttgaaaataccctcgtatcgtgctcgtaactgacttttagccgttgcttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAGATGTATTTATCTCTTCATTTCCTTCTTAAAGTTTAGCAAGTCGGGCTCA

Basic information

species Zea mays
transcript GRMZM2G460078_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460078_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 16
--gtggggacatgatgtccttgaaaataccctcgtatcgtgctcgtaactgacttttagccgttgcttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATG--TGTATAGATGTATTTATC-TCTTCATTTCCTTCTTAAAGTTTAGCAAGTCGGGCTCA
| ||| | || | | | | | || | | | | || ||| || | |||||| | |||||| ||||||||||||||||||||||| ||||||||||||| || | | | | | || | | || || | || ||| | | |
gtgcgggctgaaaattttttcttctttgcagttgtgttgagtttgttacttacct------attgcttttatcagGTCAACAAGAAGGAGCTGAAGAAATTATTAGGAGCTTAGCTGTGGTTCCAGGAAGGCAGACATTGTAATGGTTAGCTAATAAATATTTTTCGCATTGATA---
















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|6601765|gb|AW256206.1|AW256206
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|5847518|gb|AW000597.1|AW000597
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|87153333|gb|DY398122.1|DY398122
EST:     CAACAAGACTATACTTGTTGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|32945399|gb|CF050218.1|CF050218
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|32867326|gb|CF007008.1|CF007008
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|166631378|gb|EG255927.1|EG255927
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|32940106|gb|CF044925.1|CF044925
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|37385309|gb|CF629791.1|CF629791
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|17921701|gb|BM259352.1|BM259352
EST:     CAACAAGACTATACTTGTTGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|37377992|gb|CF625646.1|CF625646
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|37392249|gb|CF633373.1|CF633373
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|18177865|gb|BM379075.1|BM379075
EST:     CACCAAGACTATACTTGTGGGATTCTCTTCCTCGAAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCAGGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|91049610|gb|EB160028.1|EB160028
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGCGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|93012881|gb|EB638401.1|EB638401
EST:     CAACAAGACTATACTTGTGGGATTTTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|211208064|gb|FL437175.1|FL437175
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|17970088|gb|BM276854.1|BM276854
EST:     CAACAAGACTATACTTGTTGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
EST: gi|71533933|gb|DR784692.1|DR784692
EST:     CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAG                         GTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG
genomic: CAACAAGACTATACTTGTGGGATTCTCTTCCTCGGAATGCCATGGGAAAGgtggggacat ... cttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaataccctcgtatcgtgctcgtaactgacttttagccgttgcttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAGATGTATTTATCTCTTCATTTCCTTCTTAAAGTTTAGCAAGTCGGGCTCA
                          aactgac  putative branch site (score: 2)
 cttatttc  putative PPT
 ttatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggggacatgatgtccttgaaaataccctcgtatcgtgctcgtaactgacttttagccgttgcttatttcagGTTAACAAGAAGGAGCTGAAGAAATTGTTAGGAGCTTAGCCATGTGTATAGATGTATTTATCTCTTCATTTCCTTCTTAAAGTTTAGCAAGTCGGGCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG