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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccttccagacatttgtttctgtagtctgtgtgatcatctgatatatcatgcacatgatttagtgcttcttctatttgtttgaattttttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG

Basic information

species Zea mays
transcript GRMZM2G370852_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 9
----tttccttccagacatttgtttctgtagtctgtgtgatcatctgatatatcatgcacatgatttagtgcttcttctatttg-tttgaattttttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG
     ||   |  | ||     |     ||  |||| ||||       | | ||   | |    | |      |||| || ||| ||| | |   || | | ||||||| ||||||||||||||||||||||||| ||| ||||||||||  ||||||||
aatagttaaattgaaac-cgcataagcataagctgt-tgatgtctctctctctctctctctctctctc---tctcttatacttgatttcactacatttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG
















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|32840108|gb|CD979789.1|CD979789
EST:     GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGNTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
EST: gi|16916456|gb|BM072849.1|BM072849
EST:     GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
EST: gi|32846022|gb|CD985703.1|CD985703
EST:     GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
EST: gi|31350830|gb|CD435187.1|CD435187
EST:     CTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACT-GAGCCCAGTAGTTG
genomic: CTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAG-CCAGTAGTTG
EST: gi|32840107|gb|CD979788.1|CD979788
EST:     GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
EST: gi|166592875|gb|EG279335.1|EG279335
EST:     ATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: ATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
EST: gi|211350370|gb|FL368852.1|FL368852
EST:     GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
EST: gi|211524232|gb|FL397627.1|FL397627
EST:     GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTCACGCCAG                         ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC
genomic: GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactatag ... ttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcatgcacatgatttagtgcttcttctatttgtttgaattttttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG
                                         ttttttctctcc  CT-rich tract
                          ttctatttgtttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccttccagacatttgtttctgtagtctgtgtgatcatctgatatatcatgcacatgatttagtgcttcttctatttgtttgaattttttctctccagATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAG

- - - -ccagaca
- - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatt