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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgctctcgaattacaatattactacatccgttctcgaatatttatcgtccgctagttcatttttgaactaaaacgtgacaaataaaaaagaacggagggagtactttttatgatatggtagtaaatatgtgtggcatgcatgttttcttatggtttgaacttgtttgtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG

Basic information

species Zea mays
transcript GRMZM5G830874_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830874_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g08270.6 (Oryza sativa), 3'ss of exon 4
gtagtgctctcgaattacaatattactacatccgttctcgaatatttatcgtccgctagttcatttttgaactaaaacgtgacaaataaaaaagaacggagggagtactttttatgatatggtagtaaatatgtgtggcatgcatgttt-tcttatggtttgaacttgtttgtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG
                                                                                      ||     |||   |    | |  |||| | ||       | |     |    ||||| | |||  ||||||||| |||||||| |||||| | ||||| ||  | |||||||||||||||||||| |||||||||||||||||| || |||||  |||| ||||||
-------------------------------------------------------------------------------------gtagtgttgaatt-ataatgcatgttttttcatggacctatcacagcata---catgcctatttaccttatggtt-gaacttgtctgtgatgacagCAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG
















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|20208417|gb|BQ134506.1|BQ134506
EST:     CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGG                         CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
genomic: CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGGgtagtgctct ... gtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
EST: gi|78124910|gb|DV543294.1|DV543294
EST:     CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGG                         CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
genomic: CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGGgtagtgctct ... gtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
EST: gi|71418229|gb|DR804377.1|DR804377
EST:     ATGGCTGGAATTCAGACAGGA-CAGCTTGGGCTTGAAAGTGACGCTGAGG                         CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
genomic: ATGGCTGGAATTCAGACAGGACCAGCTT-GGCTTGAAAGTGACGCTGAGGgtagtgctct ... gtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
EST: gi|78110728|gb|DV529126.1|DV529126
EST:     CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGG                         CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
genomic: CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGGgtagtgctct ... gtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
EST: gi|78543868|gb|DV621366.1|DV621366
EST:     CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGG                         CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
genomic: CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGGgtagtgctct ... gtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
EST: gi|60400536|gb|DN233343.1|DN233343
EST:     CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGG                         CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
genomic: CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGGgtagtgctct ... gtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
EST: gi|211376348|gb|FL146641.1|FL146641
EST:     CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGG                         CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC
genomic: CATGGCTGGAATTCAGACAGGACCAGCTTGGCTTGAAAGTGACGCTGAGGgtagtgctct ... gtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatatgtgtggcatgcatgttttcttatggtttgaacttgtttgtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG
                     ttttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgctctcgaattacaatattactacatccgttctcgaatatttatcgtccgctagttcatttttgaactaaaacgtgacaaataaaaaagaacggagggagtactttttatgatatggtagtaaatatgtgtggcatgcatgttttcttatggtttgaacttgtttgtgataatagCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG