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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctttatttatttcttcagtgctagaacaaaaacagtgtgaataacatgagtgcaagaatttaacctgaccctattgcaccatttaacttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGT

Basic information

species Zea mays
transcript GRMZM5G824944_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 3
------actctttatttatttcttcagtgctagaacaaaaacagtgtgaataacatgagtgcaagaatttaacctgaccctattgcaccatttaacttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGT
      | ||| |  ||||||||||  |        |  || ||||||||       |  |  || ||| |||      || ||  |||||||||||| |||||||||||| |||||||| || |||||||| ||||| || ||||||||||| |||||||| ||||||||||| || |||||| |||||||||||||||||||||
atgggaattctgtgcttatttcttccatct------acgaagagtgtgaaggttgaaatcgtcagcattaaactgatgtctgttctaccatttaacttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGT
















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|37374265|gb|CF623478.1|CF623478
EST:     TTTGACGCTGTNGTCTGCACACACCCATGCCCCATGGTGGTAAAGGAGCG                         GTGGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
genomic: TTTGACGCTGTTGTCTGCACACA-CCATG-CCCATGGTGGTAAAGGAGCGgtgagttctc ... ttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
EST: gi|67016604|gb|CO445353.1|CO445353
EST:     CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCG                         GTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
genomic: CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCGgtgagttctc ... ttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
EST: gi|32857153|gb|CD996834.1|CD996834
EST:     CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCG                         GCTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
genomic: CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCGgtgagttctc ... ttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
EST: gi|211371831|gb|FL183018.1|FL183018
EST:     CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCG                         GTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
genomic: CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCGgtgagttctc ... ttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
EST: gi|37387441|gb|CF630914.1|CF630914
EST:     TTTTGACGCTGTTGTCTGCACACACCATGCCCCATGGTGGTAAAGGAGCG                         GTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
genomic: TTTTGACGCTGTTGTCTGCACACACCATG-CCCATGGTGGTAAAGGAGCGgtgagttctc ... ttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
EST: gi|40335763|gb|CK369833.1|CK369833
EST:     CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCG                         GTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
genomic: CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCGgtgagttctc ... ttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
EST: gi|67033495|gb|CO462244.1|CO462244
EST:     CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCG                         GTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT
genomic: CTTTTGACGCTGTTGTCTGCACACACCATGCCCATGGTGGTAAAGGAGCGgtgagttctc ... ttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgagtgcaagaatttaacctgaccctattgcaccatttaacttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGT
                                            cttattttc  CT-rich tract
                                      atttaacttattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctttatttatttcttcagtgctagaacaaaaacagtgtgaataacatgagtgcaagaatttaacctgaccctattgcaccatttaacttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - gtgctag
- - - - - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - aataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - gtgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaccat