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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttcttaaatctcatatttcagtttgacctttttcattgcactagcctctcttaacctttcttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAACTCAACTGGAGGATGAGTTCAAGAAGTTTGGTACCATCAAGCAAAATGG

Basic information

species Zea mays
transcript GRMZM2G091995_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091995_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g29480.1 (Oryza sativa), 3'ss of exon 5
gtgtttctta-aatctcatatttcagtttgaccttt-------ttcattgcactagcctctcttaacctt----tcttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAACTCAACTGGAGGATGAGTTCAAGAAGTTTGGTACCATCAAGCAAAATGG
|| |||  || ||||  ||  ||   |     || |       |  |||    |||| ||||| ||| ||    | |  ||| ||| ||| || ||||| || || ||||||| | ||||  |||||||||||   || ||||||||||||||||||||||||||||| ||||| || |   ||||
gtattttctacaatcctatgctttgatcaatactctagatatgtcaattctgttagcttctctgaactttggtctttattttgaagTTGATGCACATGCGATATACGTGAGGAGTCTACCATTAAATGCCACTACGACACAACTGGAGGATGAGTTCAAGAAGTTTGGCACCATAAAACCTGATGG
















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|211453318|gb|FL456386.1|FL456386
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|22490771|gb|BU050694.1|BU050694
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|19436283|gb|BM952693.1|BM952693
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|19058851|gb|BM737518.1|BM737518
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|87153443|gb|DY398232.1|DY398232
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|19436282|gb|BM952692.1|BM952692
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|19436716|gb|BM953126.1|BM953126
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|19058852|gb|BM737519.1|BM737519
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|19436715|gb|BM953125.1|BM953125
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
EST: gi|22490983|gb|BU050906.1|BU050906
EST:     GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAG                         ATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA
genomic: GCTGCCTTTTAGTTCCAACCCTGAGAACGGCAATATCCAAGAGCCTGAAGgtgtttctta ... ttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagtttgacctttttcattgcactagcctctcttaacctttcttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAACTCAACTGGAGGATGAGTTCAAGAAGTTTGGTACCATCAAGCAAAATGG
                                 tcttaac  putative branch site (score: 2)
                         ctagcctctcttaacc  CT-rich tract
             tttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttcttaaatctcatatttcagtttgacctttttcattgcactagcctctcttaacctttcttcttttaagATGACGCGCATGCAATCTATGTGAGGAATTTACCTCTAAATGCCACTGAAACTCAACTGGAGGATGAGTTCAAGAAGTTTGGTACCATCAAGCAAAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA