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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatttgcaaacgtctctgcctcag

Basic information

species Zea mays
transcript GRMZM2G095141_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095141_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 7
GCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatttgcaaacgtctctgcctcag
 |||   ||||  | ||||| || || |||||||||||||| |||  |||||| |||||||||||||| ||||| ||||||| |||||| || ||||||||| |     || || | | ||||| | ||      | |  ||   |  ||        | || | |   | |  |  |   ||    ||||| | ||  |     || |||                   
ACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtat-----tgattttgt-tgcctttactgctttcagcatgtcatttcctggtttatatatttttgc--gcatttaaaactactt-tcaaaagcgatgat----acgtttttt-----------------

upper sequence: GRMZM2G095141_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g04210.2 (Oryza sativa), 5'ss of exon 6
GCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatt-tgcaaacgtctctgcctcag
 |||   ||||  | ||||| || ||||||||||||||||| |||  |||||| ||||||||||| || || || ||||||| |||||| || |||||||||     |||| || | | ||||| |  |      | |  |               | ||| ||||    ||| |       || |   |||||||   | |  | |||  | |  |  | |         
ACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATTTCACTTGGAGACACGATTGGTGTTGGTACACCAGgt-----actgattttgt-tgcctttattgctttcagcatgc--------------catttcctggttcatacatttttg--cccgtttaaaactacttttaaagtgatgataccgattttt---------
















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|5761976|gb|AI967024.1|AI967024
EST:     TGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: TGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|211227159|gb|FL464265.1|FL464265
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|71301050|gb|DR786554.1|DR786554
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|211088485|gb|FL432076.1|FL432076
EST:     GAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|149072591|gb|EE157105.2|EE157105
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|91872712|gb|EB402669.1|EB402669
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|110950579|gb|EE170731.1|EE170731
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|76016845|gb|DT944015.1|DT944015
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|31911304|gb|CD651858.1|CD651858
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|71318555|gb|DR796038.1|DR796038
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|211013342|gb|FL464501.1|FL464501
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|211139185|gb|FL464627.1|FL464627
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|148950048|gb|EC895580.2|EC895580
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
EST: gi|211081279|gb|FL464186.1|FL464186
EST:     GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAG                         GTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA
genomic: GGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactact ... tctgcctcagGTAGCGTGGTTGCTATGCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatttgcaaacgtctctgcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC