Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctcgccttccccatctcatcctcccttatcgatctggtgattactctacctgtctactcctaaattcccgattcgcttcattccgcggccgccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG

Basic information

species Zea mays
transcript GRMZM2G019267_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 1
gtaacctcgccttccccatctcatcctcccttatcgatctggtgattactctacctgtctactcctaaattcccgattcgcttcattccgcggccgccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG
||||   |   |  | ||   | |   |    |||||   || |||| |||     ||||  |  |  |||| |   |||||        || |||  |     |||||||| |||||||| ||||||||||  || |||||||||||||||||||||||||||||||||||||||||||||||||| 
gtaaaaacatttcgctcaaaccctagccatgaatcgag--ggggattgctc-----gtctgat--tggattctct-ctcgct--------cgcccgttgtt--tagGCAAGTTTACATGGCCAAGGAGACGGAGACGAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGC
















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|211438450|gb|FL012012.1|FL012012
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438447|gb|FL012009.1|FL012009
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|89248442|gb|DY620228.1|DY620228
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|29130258|gb|CB380962.1|CB380962
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|148931632|gb|EC874770.2|EC874770
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438457|gb|FL012019.1|FL012019
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211435860|gb|FL012004.1|FL012004
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGC-GATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGAC-GGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438453|gb|FL012015.1|FL012015
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|148946782|gb|EC892051.2|EC892051
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438455|gb|FL012017.1|FL012017
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|148938174|gb|EC882457.2|EC882457
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|110209027|gb|EC890924.1|EC890924
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211002224|gb|FL012020.1|FL012020
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438454|gb|FL012016.1|FL012016
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211435853|gb|FL011997.1|FL011997
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438448|gb|FL012010.1|FL012010
EST:     GCGTAGACTGCTTCGAGAATGCTCGAGCAGATCGGCGAGGGCWCCTACGG                         GCAATGTGTACATGGCGAAGGAGATCGGGCACCAACGAGATCGTCGCGCTC
genomic: GCGTAGACTGCTTCGAGAA-GCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAA-GTGTACATGGCGAAGGAGA-CGGGCACCAACGAGATCGTCGCGCTC
EST: gi|211438445|gb|FL012007.1|FL012007
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438446|gb|FL012008.1|FL012008
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438452|gb|FL012014.1|FL012014
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438444|gb|FL012006.1|FL012006
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211435855|gb|FL011999.1|FL011999
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGANGATCGTCGCGCTCA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGA-GATCGTCGCGCTCA
EST: gi|211435856|gb|FL012000.1|FL012000
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211435858|gb|FL012002.1|FL012002
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211002225|gb|FL012021.1|FL012021
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGNCGAGGGCACCTACGN                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211435854|gb|FL011998.1|FL011998
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGAC-GGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|148942610|gb|EC887630.2|EC887630
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
EST: gi|211438456|gb|FL012018.1|FL012018
EST:     AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGG                         GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA
genomic: AGCGTAGACTGCTTCGAGAAGCTCGAGCAGATCGGCGAGGGCACCTACGGgtaacctcgc ... ccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctgtctactcctaaattcccgattcgcttcattccgcggccgccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG
           tcctaaa  putative branch site (score: 2)
              taaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctcgccttccccatctcatcctcccttatcgatctggtgattactctacctgtctactcctaaattcccgattcgcttcattccgcggccgccgccggcagGCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA