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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggtacaatttaaccaatgtggtcgttttgttattctacctcttgttttttgttgccagacataatatattagtgttgtgtgttatttttcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCTCGTGACAAGGAAACTAG

Basic information

species Zea mays
transcript GRMZM2G175676_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175676_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 2
ctggtacaatttaaccaatgtggtcgttttgttattctacctcttgttttttgttgccagacataata-------tattagtgttgtgtgttatttttcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCTCGTGACAAGGAAACTAG
        |||| || |   | ||  || || || | |  ||||||||||| ||   |||  | ||||       || |   | |   | |||||||||||||||||||||||||||||| ||||| |||||||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||| 
------atatttcacaatgattgttcttatgctactttgtctcttgttttt-gtcttcagctacaataagctgtataatttcgctaactcttatttttcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA

upper sequence: GRMZM2G175676_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0109g00370.t01 (Vitis vinifera), 3'ss of exon 1
ctggtacaatttaaccaatgtggtcgttttgttattctacctcttgttttttgttgccagacataatatattagtgttgtgtgttatttt--tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCTCGTGACAAGGAAACTAG
    |   ||||| |     |  |  |   |||||| ||  |  |  ||  | |    || | |||  | ||    |||  | | ||||   |  || |||||||| |||||||| | |||    ||||||||| ||||||| ||||| |||||||||||  | || || ||| || |||| ||||||||||||||||||  
agcatgttatttatctgcctttatgttcaagttatt-taaataataattcatataaaaaggc-taacgtgttttaattggttttaatttcaattgtacatagGTAATTTGGATGAGAGGGTAAGCGAGAGGGTTTTGTATGATATTCTGATTCAGGTAGGGAGGGTGGTGGACTTATACATCCCTCGTGACAAGGAAACTGA
















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|32796494|gb|CD948730.1|CD948730
EST:     GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|211439602|gb|FL298833.1|FL298833
EST:     CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|32790458|gb|CD942694.1|CD942694
EST:     GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|33104379|gb|CF064339.1|CF064339
EST:     GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|211439601|gb|FL298832.1|FL298832
EST:     CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAWATTCTTATTC
genomic: CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|32799252|gb|CD951488.1|CD951488
EST:     GGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: GGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|32797760|gb|CD949996.1|CD949996
EST:     GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: GATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|211439598|gb|FL298829.1|FL298829
EST:     CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
EST: gi|211439607|gb|FL298838.1|FL298838
EST:     CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGG
genomic: CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGG
EST: gi|211009131|gb|FL298877.1|FL298877
EST:     CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAG                         GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC
genomic: CCCAGATCCGGCGGCCATGGCAAGGAACCCGGGCTGCACCGTCTTCATAGgtgagatctc ... tcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttgttgccagacataatatattagtgttgtgtgttatttttcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCTCGTGACAAGGAAACTAG
                                      ttatttttctt  CT-rich tract
                                    tgttatttttcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggtacaatttaaccaatgtggtcgttttgttattctacctcttgttttttgttgccagacataatatattagtgttgtgtgttatttttcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCTCGTGACAAGGAAACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA