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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccttgcattgcttgtacaggaaatctttttttttcagatttgaaaatgtatcattgcataataatttgtgcatgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGCGATCTTGCTTCAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAA

Basic information

species Zea mays
transcript GRMZM2G373175_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G373175_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 11
gtatgttc-cttgcattgcttgtacaggaaatctttttttttcagatttgaaaatgtatcattgcataataatttgtgcatgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGCGATCTTGCTTCAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAA
||| ||||  ||| ||| ||| |           || ||  | | ||  | ||| |||  ||||  ||||  ||  | ||||||| |||||||||| || |||||||||||||| ||||||||||||||||||| ||| |||||||| ||||||||  ||||| | ||||| |||||||| |||||||
gtaagttcatttgaattacttat-----------ttgttgctgaaataagcaaaggtactattggctaatttttacttcatgctgcagGATGGACATTTGAAAATGCTTGGAGGATATCTTGAGTTCTTCATGAGTCGTGATCTTGCATCAACTTACTTGAGTCTCAAGAGTGAACTTGATAATTTAA
















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|211272990|gb|FL022928.1|FL022928
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|211272993|gb|FL022931.1|FL022931
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGGTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|211272997|gb|FL022935.1|FL022935
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|13316191|gb|BG410638.1|BG410638
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|211272995|gb|FL022933.1|FL022933
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|211272996|gb|FL022934.1|FL022934
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGNACACTCNAAAATGCTTGGAGGTTATCCTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|211272991|gb|FL022929.1|FL022929
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|31352989|gb|CD437346.1|CD437346
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|211272994|gb|FL022932.1|FL022932
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|211272992|gb|FL022930.1|FL022930
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
EST: gi|13316192|gb|BG410639.1|BG410639
EST:     CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTG                         GATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC
genomic: CTGATTCTATACTGTTGTTATTCGGAGGCTGCATAAAACAAGGGGGCTTGgtatgttcct ... catgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttcagatttgaaaatgtatcattgcataataatttgtgcatgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGCGATCTTGCTTCAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAA
                           attgcataataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttccttgcattgcttgtacaggaaatctttttttttcagatttgaaaatgtatcattgcataataatttgtgcatgctgtagGATGGACACTTAAAAATGCTTGGAGGTTATCTTGAGTTCTTCATGAATCGCGATCTTGCTTCAACTTATGTGAGTTTGAAGAGAGAACTTGAGAATTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA