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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaaatgatacacagagtataagcttctataattttggcaatccttcacttcaattctcttcctcagtcctcactgttgtacttctgattttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG

Basic information

species Zea mays
transcript GRMZM2G079538_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 1
cacaaatgatacacagagtataagcttctataattt-tggcaatccttcacttcaattctcttcctcagtcctcactgttgtacttctgatttt-cctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG
||  ||||      |   |  | | || |   || | |  |  |   |   ||   |||| ||  |     || |||  |||| |||||||||  | ||||||| ||||||||| | ||||||||| |||||| ||| | ||||| ||||||||||||||
cagcaatgtatttaattctgcatgtttatggcatctattactttgtgttcgttagcttcttttttttttgtcttact-ctgta-ttctgatttgacttgcagACTCTAGGCCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAG
















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|148950981|gb|EC896624.2|EC896624
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211169879|gb|FL077608.1|FL077608
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211325989|gb|FL407943.1|FL407943
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211233035|gb|FK998528.1|FK998528
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|148943959|gb|EC889039.2|EC889039
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|31355469|gb|CD439826.1|CD439826
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAG
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|31355590|gb|CD439947.1|CD439947
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAG
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|78111553|gb|DV529950.1|DV529950
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|149015063|gb|EE044815.2|EE044815
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|149009740|gb|EE041651.2|EE041651
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|78103875|gb|DV522298.1|DV522298
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|148958216|gb|EC904424.2|EC904424
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|148991485|gb|EE033000.2|EE033000
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|149081048|gb|EE170148.2|EE170148
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211169872|gb|FL077601.1|FL077601
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCCCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|148931436|gb|EC874404.2|EC874404
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|31358640|gb|CD442997.1|CD442997
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAG
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211230977|gb|FK998519.1|FK998519
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGG-SCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|148978727|gb|EE026283.2|EE026283
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|149014456|gb|EE044070.2|EE044070
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|149003557|gb|EE038930.2|EE038930
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211321201|gb|FL380429.1|FL380429
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|31353408|gb|CD437765.1|CD437765
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAG
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211169881|gb|FL077610.1|FL077610
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|67033243|gb|CO461992.1|CO461992
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
EST: gi|211169620|gb|FL396011.1|FL396011
EST:     GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCC                         ACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA
genomic: GAATGGCGTCCCGCGTCGCCTCGGGCCTCCTCCGCCGCCGCGCCGGCGCCgtaatgccct ... tttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttcaattctcttcctcagtcctcactgttgtacttctgattttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG
                                     cttctgattttcct  CT-rich tract
     ttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaaatgatacacagagtataagcttctataattttggcaatccttcacttcaattctcttcctcagtcctcactgttgtacttctgattttcctgcagACACTAGGCCTCCTAAGGAGTTATGCACATGTCAGAAGCTACAACAGTCAACTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - -gatacac
- - - - - - - - - - - agcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctga