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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataccgcatcagcagaaagtccttagctaaattcaacctgcttgtattttctaggtctaatgatcgtaaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA

Basic information

species Zea mays
transcript GRMZM2G099547_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099547_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 3'ss of exon 3
--------------gtatataccgcatcagcagaaagtccttagctaaattcaacctgct--tgtattttctaggtcta-atgatcgtaaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA
                ||   ||   | | |   |  || ||||     || |  ||  |  |  || ||||| |   | |  |   | |||  ||||||||| |||||||| ||||||||||||||| |||||||||| |||||||||||||||||||| || ||||||||||||||||| |||||||||||||
gtattaccaatttaccatgagccatgtgaactata--tcattagtcct-tttagtctattattccatgttctaagctaacaacactttgaaatggcagGATGCACCTGTACCACCTTGCATCACACAATTGGAAGGTGGCCTTGTCCAAGTAGCCATTGAGGTTGAAGACCGGGCACAACGGTCAGCAATAACAA

upper sequence: GRMZM2G099547_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 3
gtatataccgcatcagcagaaagtccttagct--aaattcaacctgcttgtattttctaggtctaatgatcgtaaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA
||| | |  |  |    | ||  |  | |  |  ||  ||||      |  ||     |  | |  ||   | |      |||||||| || |||||||| |||||  ||||||| || ||||||||||| || || || || |||||||||||||| ||||||||||||||||| ||||
gtaca-attggtttcttataatcttttcaattccaagatcaaa--aactagatcactaatctgttgtggcggca----cacagGATGCACCAGTACCTCCCTGCATTTCACAACTCGACGGTGGACTTGTTCAGGTTGCAATAGAAGTGGAAGACCGTGCACAACGTTCAGCAATCACAA

upper sequence: GRMZM2G099547_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtatata--ccgcatcagcaga----aagtccttagctaaattcaacctgcttgtattttctaggtctaatgatcgtaaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA
                |||  |   | |||||          || | ||    ||  |  || |||     ||||  |  |     ||||       ||  ||||||||||||| |||||||||||  ||||  | ||||| || ||||||||||| || || || ||||||||||| |||||||| || ||||| ||||
ttttatacttctatgagtagttgatctgcatctttgttttccaaattctcgaatagttataaactgtggaaatttgttttggactctgatttc---tctctagGATGCTCCTGTGCCTCCTTGCATATCACAGTTAGAAGGGGGGCTTGTCCAAGTGGCAATAGAGGTGGAAGACCGTGCACAACGCTCTGCAATTACAA

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|15199102|gb|BI423657.1|BI423657
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGA
EST: gi|94477735|gb|EB706693.1|EB706693
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGGAGGTGGACTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|78180203|gb|DV550576.1|DV550576
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGAGTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|12045537|gb|BF727676.1|BF727676
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGA
EST: gi|149104413|gb|EE289858.2|EE289858
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|71433975|gb|DR815025.1|DR815025
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|71450211|gb|DR831261.1|DR831261
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|50325142|gb|CO520268.1|CO520268
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|84351516|gb|DW245921.1|DW245921
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGATACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|60337078|gb|DN204051.1|DN204051
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|19822251|gb|BQ048275.1|BQ048275
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGAGTTGTCCAA
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAA
EST: gi|71435787|gb|DR816837.1|DR816837
EST:     ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACAT                         GATGCTCCTGTACCTCCTTGCAT
genomic: ACGTTATTGACGGAGCACTGAGTTCAGTTGCTGCTGAGACAAATCCACATgtatataccg ... aaaactgcagGATGCTCCTGTACCTCCTTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagctaaattcaacctgcttgtattttctaggtctaatgatcgtaaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA
                                gtctaat  putative branch site (score: 3)
     taaattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataccgcatcagcagaaagtccttagctaaattcaacctgcttgtattttctaggtctaatgatcgtaaaactgcagGATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA