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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctctgtttccaaatgttttgtaccaccccccgttcccattggatgttctccttggagttctggacctgtattatagtggctgctaactgtagctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATCATCCTCAACTTTGTCAGATTCATTGAGGAACTGGAGAAGCAGCGTTCGT

Basic information

species Zea mays
transcript GRMZM2G325131_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G325131_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g38950.1 (Oryza sativa), 3'ss of exon 7
--gtacctctgtttccaaatgttttgtaccaccccccgttcccattggatgttctccttggagttctggacctgtattatagtggctgctaactgtagctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATCATCCTCAACTTTGTCAGATTCATTGAGGAACTGGAGAAGCAGCGTTCGT
   ||  |||   || ||||| || |  ||||     | |  |  || |    | ||        |    || |  || |  | | ||  ||  | | |   |||||||| |||||||||||||| ||||||||||||||||| ||||||||||  ||||| |||||||| || || ||||| ||||| ||||||||||||||| |  
gtatatatctaaatc-aaatgcttggcgccaca----gctttcgatgtacaccccccccccccccccccccccgagttgttattgatgtcaatggcatca--tttcagGGAGTCCAATTCCACCCAGAGAGCATCATCACCCCAGAAGGCAAGAGGATCATTCTCAACTTCGTGAGGTTCATCGAGGAGCTGGAGAAGCAGCGTGCCG
















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|32925512|gb|CF030324.1|CF030324
EST:     TACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAACATCATCACCCCTGAAGGCAAGAAAATC
genomic: TACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32926357|gb|CF031169.1|CF031169
EST:     ACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: ACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32926358|gb|CF031170.1|CF031170
EST:     ACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: ACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|40334289|gb|CK368359.1|CK368359
EST:     AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|211435759|gb|FL463295.1|FL463295
EST:     AGATGGACTTATCATGGTTGCTCGCCACAAGAAGTACAAACACATCCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAAT
genomic: AGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACAT-CCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAAT
EST: gi|32925173|gb|CF029985.1|CF029985
EST:     TACAAACACATCCAG                         GGTGTCCAATTCCGCCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: TACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32925121|gb|CF029933.1|CF029933
EST:     ACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: ACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|37377729|gb|CF625495.1|CF625495
EST:     AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32924671|gb|CF029483.1|CF029483
EST:     TACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: TACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|78021212|gb|DV489599.1|DV489599
EST:     AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|78113402|gb|DV531794.1|DV531794
EST:     AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|33103571|gb|CF063531.1|CF063531
EST:     GTACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: GTACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32926406|gb|CF031218.1|CF031218
EST:     ACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: ACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32942025|gb|CF046844.1|CF046844
EST:     GTACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: GTACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32925654|gb|CF030466.1|CF030466
EST:     ACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: ACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32925818|gb|CF030630.1|CF030630
EST:     TACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: TACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32925314|gb|CF030126.1|CF030126
EST:     TACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: TACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|78105962|gb|DV524380.1|DV524380
EST:     AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: AAGATGGACTTATCATGGCTGCTCGCCACAAGAAGTACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
EST: gi|32926489|gb|CF031301.1|CF031301
EST:     ACAAACACATCCAG                         GGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC
genomic: ACAAACACATCCAGgtacctctgt ... ctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttggagttctggacctgtattatagtggctgctaactgtagctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATCATCCTCAACTTTGTCAGATTCATTGAGGAACTGGAGAAGCAGCGTTCGT
                                 tgctaac  putative branch site (score: 1)
                                             ctgttttc  putative PPT
                   tgtattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctctgtttccaaatgttttgtaccaccccccgttcccattggatgttctccttggagttctggacctgtattatagtggctgctaactgtagctgttttcagGGTGTCCAATTCCACCCGGAGAGCATCATCACCCCTGAAGGCAAGAAAATCATCCTCAACTTTGTCAGATTCATTGAGGAACTGGAGAAGCAGCGTTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC