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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag

Basic information

species Zea mays
transcript GRMZM2G116151_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttt-------tcactggtttctaca------aaaaatttctttggccttgtcatctattgcatgttc------caactggaatt-------acgtctgaactttttggccttgt---cgtccatcctgcag
|| ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| |||||||||||||||||||||||||||||   ||||||| |  ||| |       |||   |||| |  |      | ||  ||  |  ||||||  ||    | ||  ||       || |||| |||        | |   ||| ||||     |||   | |||||   ||||
GTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAAgtaagtgacat-tttgtccattttttctggcatgatcaactgtttttttattcagcacaacctttgtccgccttgctattctgtacacattttgatggcagctggcattctagaatgcatactaacattttctttctgtaaacatccatttggcag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag
|| ||  | |||||||| ||| ||| ||||||||| ||||| |||||  |||| ||||||||||| |||||||||| |||     |||| | |||||  ||          ||| |      |||      | || ||||     | || ||  ||||   |||| || | ||||||  |    |    |  ||| || ||
GTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAAgtgagttcactattttttcttcccgttgc--------tctgctggggtttt-----actttatcat-----ggatatt--aact---attaagtgttaactttgcgatgat----tatatcttgtag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag
|| ||  | |||||||| ||| ||| |||||| || ||||| |||||  |||| ||||||||||| |||||||||| ||        ||  |  |  ||| ||| |     ||| |      |||      | || | ||  ||   | || | ||||      | |  |  |  || | |                    
GTAGCCTTAAAATTTGAGCATAGAAGCAGCAAGGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAAgtgag--------ttcactattttttcttcgcgttgctctgctggggtttt-----actttattatggatactaagtgctaactatg-ccatgattatatcttgtag--------------------

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaac---tggaattacgtctga-actttttggccttgtcgtccatcctgcag
|| ||  | || ||||| ||| ||||||||||||| || ||||||||  | || |||||||||||||||||||||| || |      || |  |  || || ||  ||| |     |  |    ||||  || |  |||  || |   | |   ||    ||  || ||   |||  |||| |   ||  |||||||        
GTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAAgtgagcg------ttatggt--ctcttgtctttggctc---taggattcatcttctgcttgttcaaatagtttgtttataaaaggatgagataactaatgatgctttatcatctgttcgtccag-------

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag
|||||  | |||||||| ||| ||| ||||||||| ||||| |||||  | || |||||||||||||||||||||| ||  |     |  |   | ||| | |  ||| ||          || | ||   || ||  | |||||| || |      |  |  |  |   | | | ||||   |  | |    ||||||||
GTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAAgtgaggcatcttctgatttcttcttatctgtctgatt-------ggcatgtatt---ccatggtagctattggatat-----atatacatgtgatggtattatttgctttctttgatt-tcctgcag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcat-ctattgcatgttccaac-tggaa-ttacgtctgaactttttggccttgtc-gtccatcctgcag-------------------------------------
|| ||  | || ||||||||||| | |||||| |||||||| |||||| ||||||| |||||||||||||||||||  ||  || |      |   | ||| | |    || ||||||    | || ||||  |||   | | | | |  |   || | ||||  |||  | ||  || |  ||     ||     |      |                                      
GTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAAgtgcgtctcgaaccgactcagtcctttct-atcctttgctacaa----tgtcattggaattgctgttccaattctagcctcatcgtggaggttatttttgtgctgtcgggttcaatctaattaggtcataaatgttaatggtgatgataatccttggttgttgcgcag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S613_17V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgt-ccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag
               |   | ||| || || ||||| |   | || || | |||  ||||| |||||| ||||||||||||||||||||  ||  ||   | || || |  |  ||||||   | |    |    ||| ||                                                                          
GTTGCGGGGTTGAAGTTTGAGCAAGTTCGAGCATCGGAGTGgtaagggctacaatcatggtcctccttgtgagtggcaagtttacaagtgcgtctcgagctcgtaccattgtgatttcac---tcttcggatgtgattactagt-----------------------------------------------------------------------

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgt-ccttccttttttcact----------ggtttcta-caaaaaatttctttggccttgtcatctattgcatgttccaactggaattacg--------tctgaactttttggcct-tgtcgtccatcctgcag
|||||  | || || || ||||| |  || || || ||||| |||||| |||||||||||||||| ||||||| ||  ||  |    |||| || |  |  |||||||          | || |||       ||||   |  |  | |    ||||        ||| ||  |||| |         || | |||  ||||    |  |  | | ||||||
GTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACACgtgcgtctcaagcttgtaccattgtgatttcactcttgagatgtgattgctagtgtcgcatttacctctctgtatttcttattttcatcatcaaatgtgattagggcttgtctcctaaccttgatggctggcgcgggtctttctgcag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S208_44V6.1 (Physcomitrella patens), 5'ss of exon 3
------------GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgt-ccttccttttttcact----------ggtttctacaa--aaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag-----------
              | | | ||| || || ||||| |   | || || || ||  ||||| ||||||| |||||||||||||||||||  ||  ||   | || || |  |  |||||||          | || |||       |||| | ||       |  |   || |||  | ||| ||  |||| | ||   ||  |   |||    |     |  | |            
GTTGCGGGTTGAAGTTCGAACAAGTTCGAGCATCGGAGTGGTAACGGCTGTAATCATGGTCCTCCTTACGAGTGGCAAGTTTACAAgtgcgtctcgagctcgtaccattgtgatttcactcttgagatgtgattactagtgtcgcaattacctttctgcatttcttattttcatcattcaaatgtgattagggcttgtctcctaaacctccatggttgacgcggattctttctccag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: EFJ19085 (Selaginella moellendorffii), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag
|||||  |||| || || ||| | | |||||||||||||||||||||  ||||||| || ||||| |||||| ||| |||          |   || ||| |  | | ||||||    ||  |||  |||                                                                       
GTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGAgtgagtagttctaccatgagtcttttctcta-tagtttct----aagttttggttgatag-------------------------------------------------------------------

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 3
lower sequence: EFJ31718 (Selaginella moellendorffii), 5'ss of exon 3
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag
|||||  | || ||||||||  ||| ||| ||||| |||||||||||  |||| ||||||||||||||||||| ||| ||  |    || |   |  |||||||  ||  || |      ||  | |   |  || |  | |   |                                                       
GTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACACgtatgtagcattgttttggctttttttttctttgtgttttgtttctaagctatcgtgttttat-gtttgcag-------------------------------------------------------

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|30306558|gb|CD001231.1|CD001231
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
EST: gi|101387539|gb|EB815784.1|EB815784
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
EST: gi|211200248|gb|FK978072.1|FK978072
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
EST: gi|71767696|gb|DR965633.1|DR965633
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
EST: gi|78112677|gb|DV531071.1|DV531071
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
EST: gi|211200247|gb|FK978071.1|FK978071
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
EST: gi|149078987|gb|EE167841.2|EE167841
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCT
EST: gi|30031898|gb|CB833749.1|CB833749
EST:     ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA                         CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAA
genomic: ACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacg ... catcctgcagCACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAAgtaagtgacggatttgtccttccttttttcactggtttctacaaaaaatttctttggccttgtcatctattgcatgttccaactggaattacgtctgaactttttggccttgtcgtccatcctgcag

- - - - - - - - - - - - - - GCAAAG