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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgattcttccggacacttctgcttcatcagttttatgataattttccacacacactgattattgtgttgtgaaaatgtgattgataaacatgtatatgctgagaaatgaatcaactcttccactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTGCGGATTTGGAAAACTACCATCCAGAGGAAGGGATGATTCTTGCAAATAC

Basic information

species Zea mays
transcript GRMZM2G014376_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014376_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv14s0030g00650.t01 (Vitis vinifera), 3'ss of exon 9
gtatatgattcttccggacacttctgcttcatcagttttatgataattttccacacacactgattattgtgttgtgaaaatgtgattgataaacatgtatatgctgagaaatgaatcaactcttccactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTGCGGATTTGGAAAACTACCATCCAGAGGAAGGGATGATTCTTGCAAATAC
                                   |||| | || ||||   | | | |    | ||  |  |   || |     | |       ||  |   || | |             || ||  |  |||    |||  |||||||||| |    | |||| ||    ||  ||||||||||||| || ||||| | ||||||||| || ||||||||||||||||||||
----------------------------------cttttgttatcatttctgata-ataaatgtcatccttgttcaaataaacattggtcctttctgctttaactcaaacgatggcttgtattttcatctgacagAGAAAGCTAAAGAACTTGCAAGTAAAGTTGGGGGAGAGGCCATGACTCTTGCGGAATTAGAAAATTTCCATCCAGAAGATGGGATGATTCTTGCAAATAC
















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|58029719|gb|CX725146.1|CX725146
EST:     GCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCNCAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: GCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|18964901|gb|BM661275.1|BM661275
EST:     GAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGG-GGGCCTGCATTGACTCTTG
genomic: GAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|211212492|gb|FL066518.1|FL066518
EST:     TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|78091464|gb|DV519838.1|DV519838
EST:     TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|6056521|gb|AW090911.1|AW090911
EST:     TGGGGCAAAAGAGATTGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|87153743|gb|DY398532.1|DY398532
EST:     AAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: AAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|211212493|gb|FL066519.1|FL066519
EST:     TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|22490394|gb|BU050317.1|BU050317
EST:     GAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: GAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
EST: gi|74241889|gb|DT649803.1|DT649803
EST:     TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTG                         CACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG
genomic: TGGGGCAAAAGAGAAAGGAGCAAGAGTTGTAATTGCAAACCGTACCTTTGgtatatgatt ... cactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgattgataaacatgtatatgctgagaaatgaatcaactcttccactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTGCGGATTTGGAAAACTACCATCCAGAGGAAGGGATGATTCTTGCAAATAC
   gattgat  putative branch site (score: 4)
                                       ctcttccactttcc  putative PPT
        ataaacatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgattcttccggacacttctgcttcatcagttttatgataattttccacacacactgattattgtgttgtgaaaatgtgattgataaacatgtatatgctgagaaatgaatcaactcttccactttccagCACGAGCACAAGAACTTGCCAACTTAATTGGTGGGCCTGCATTGACTCTTGCGGATTTGGAAAACTACCATCCAGAGGAAGGGATGATTCTTGCAAATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA