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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagatttctctgctgtaaaatgtccccttgcggttttggatgaccagagagtcctgaaaactgtgatgaatctagaagggtaccgtttatttttt...

Basic information

species Zea mays
transcript GRMZM2G081812_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 2
GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgta-tgcagatttctctgctgtaaaatgtccccttgcggttttggatgaccagagagtcctgaaaactgtgatgaatctagaagggtaccgtttatttttt
|||||| |||||||||||||| ||||| ||||| ||||| ||||| ||||| ||||| || |||||| |  |||| ||||| || || ||||||||||||| |||   |      |  |  | |  | |   |     |||   |       ||| |  |   |  || | |  ||||    | |   | | |      
GGTTCCCAATGCAAAGCCTGAGAGGGAATCAACAGAGATTGAGATCTTTGGGATGCAAGGGATTCCTCCAGATGTGTTGGCCGCCCACTATGGAGAAGgtactgctattaaacacggcgacacacatgcaagtttttatttatttatttgttgagactaggctatagttaagtgtctacggtgatttagctgaaaaga-

upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G30970.2 (Arabidopsis thaliana), 5'ss of exon 2
GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagatttctctgctgtaaaatgtccccttgcggttttggatgaccagagagtcctgaaaact---gtgatgaatctagaagggtaccgtttatttttt-----
 ||||||||||| ||    | | | || ||||| || || || |||| ||||||||| ||||||||  | ||||| ||| ||||||||||||||||||  | | |    | |  | |    |  || |  ||  | ||    |||| ||     |   || || |   | ||| ||| |  | |  |     | |  | ||     
-GTTCCTAATGCTAAAGACGGTCGAGATTCAACTGATATTGAAATATATGGAATGCAAGGAATTCCACCCCATGTCTTGACTGCTCATTATGGAGAAGA-AGgtatgcatttgagatagtgagagtactgtttagatt----atgagcaattgatttagagaagtaaggcgataaatttgtatgtctcttcatcaagtgttgtaga
















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|211062251|gb|FL249756.1|FL249756
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAAGTAGAAGTGCCTCAGGTAAGG
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCC-AAAGTAGAAGTGCCTCAGGTAAGG
EST: gi|31361671|gb|CD446028.1|CD446028
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|71325031|gb|DR799198.1|DR799198
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|24462593|gb|BM660124.1|BM660124
EST:     ATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: ATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|74034907|gb|DT535397.1|DT535397
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGTCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|26457010|gb|CA828593.1|CA828593
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|211108805|gb|FL115292.1|FL115292
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|22818963|gb|BU499053.1|BU499053
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|211109705|gb|FL115302.1|FL115302
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|87155380|gb|DY400169.1|DY400169
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|26457257|gb|CA828840.1|CA828840
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|29946767|gb|CB816315.1|CB816315
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGGCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|32910104|gb|CF014916.1|CF014916
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|211108807|gb|FL115294.1|FL115294
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCA
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCA
EST: gi|26559878|gb|CA832113.1|CA832113
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|22543269|gb|BU093707.1|BU093707
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAG-GCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagatttctctgctgtaaaatgtccccttgcggttttggatgaccagagagtcctgaaaactgtgatgaatctagaagggtaccgtttatttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA