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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgatgcatgacctcaatcaattggcaagcatgtactcttcgtctgaagttgcattacatttgtatatatctaatttcttatgcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG

Basic information

species Zea mays
transcript GRMZM2G072865_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G072865_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 2
gtactgatgcatgacctcaatcaattggcaagcatgtactcttcgtctgaagttgcattacatttgtatata-tctaatttcttatgcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG
||||||||| |||  ||  || | ||  ||| ||  || |   | |     |||  ||      |  ||||| | || |||||| || | | |||||| ||| | || ||| |||||||| |||||||||| || || || || || |||||||| |||||| | |||||||||||||||||||||||||||||||
gtactgatgaatgcacttcattactt--caatcaactaatgaacatactcggttatatctttaatagatataatatagtttcttgtgtata-tcagCATTCAGCAGGCCAGCTGAGGAATCGGAAGAATTCAAACTCTGGTGGGGCCAAAGTTTCAGAAAGTACCGATATAGTTACATTTGCTGATGTGGCTGGAG
















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|32926844|gb|CF031656.1|CF031656
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32926579|gb|CF031391.1|CF031391
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32925914|gb|CF030726.1|CF030726
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGGGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32929777|gb|CF034589.1|CF034589
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32924793|gb|CF029605.1|CF029605
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32925296|gb|CF030108.1|CF030108
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32926564|gb|CF031376.1|CF031376
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA
EST: gi|32925381|gb|CF030193.1|CF030193
EST:     TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAG                         CAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCAGCGGAGCA
genomic: TTGTATTGATTGCGGTAGTTTTGCAGCGCCTGCCAATAAGCTTTTCTCAGgtactgatgc ... gcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcgtctgaagttgcattacatttgtatatatctaatttcttatgcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG
                               atctaat  putative branch site (score: 3)
                attacatttgtatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgatgcatgacctcaatcaattggcaagcatgtactcttcgtctgaagttgcattacatttgtatatatctaatttcttatgcaaactcagCAATCACCCGGTCAGTTGAGGAATAGGAAGAATTCTAATTCCGGCGGAGCAAAAGTTTCTGAAAGTTCGGATATAGTTACATTTGCTGATGTGGCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA