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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctcattctccttatttgaatggatttctctattcatcgtgtagatttcttgtttttgtgtgtgtgtcatgacatcactatgtgtttgttgttgttggaactgtaggaatacagatacagttatgtagctgaattatgactcttgcatgcag

Basic information

species Zea mays
transcript GRMZM2G052875_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g16970.2 (Oryza sativa), 5'ss of exon 2
AGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctcattctccttatttgaatggatttctc---tattcatcgtgtagatttcttgtttttgtgtgtgtgtcatgacatcactatgtgtttgtt-gttgttgga--------actgtaggaatacagatacagttatgtagctgaattatgactcttgcatgcag--------
|| ||||||||||| |  |||||||||||||| || |||||| || ||||  |||||||||||||||||||||||||||||||||||||||||||||| |||  ||| || ||   ||    ||||     || ||   | ||  | |  |    || |||     |||| | ||   | |  |     ||| | || | || | | ||        |||||||| |  |  | | || | | ||   ||||| ||  |  |   |||          
AGGGGCGGCGTGATCAGGTGCAGGGACGGATCGGGGAGGTTCGCCAGGGACAAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCAGgt--tgcttccttgctctcgcctgaaaaagattatccctttttttttgccttagctttttgcggaggtgt-tctggttttaggttctcgtgtttgtgctagtagctcgaatctacttactgtaggcaatctaagagagctgtttaatcgaattgtgtttactttttgccttggcgcag
















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|87153726|gb|DY398515.1|DY398515
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211215768|gb|FL437214.1|FL437214
EST:     CGACTTCTGCGACTGCCCCGACGGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: CGACTTCTGCGACTGCCCCGAC-GGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|22490637|gb|BU050560.1|BU050560
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322390|gb|FL223767.1|FL223767
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|19057817|gb|BM736484.1|BM736484
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|31612130|gb|CD568752.1|CD568752
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|19058293|gb|BM736960.1|BM736960
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGCCGGCACCGCCGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211320224|gb|FL223759.1|FL223759
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGGAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322386|gb|FL223763.1|FL223763
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211457195|gb|FL323091.1|FL323091
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322388|gb|FL223765.1|FL223765
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGGAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322389|gb|FL223766.1|FL223766
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|32847353|gb|CD987034.1|CD987034
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211320227|gb|FL223762.1|FL223762
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCCNTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCAC
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCG-TGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCAC
EST: gi|211320225|gb|FL223760.1|FL223760
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211320223|gb|FL223758.1|FL223758
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctcattctccttatttgaatggatttctctattcatcgtgtagatttcttgtttttgtgtgtgtgtcatgacatcactatgtgtttgttgttgttggaactgtaggaatacagatacagttatgtagctgaattatgactcttgcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA