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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcctatatatgcctcaatagactggcctcaaaaggtctggaatgttaagtgttcatttgtctgttgttcatgcttttgatctgattttctattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT

Basic information

species Zea mays
transcript GRMZM2G037342_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 11
tgcctatatatgcctcaatagactggcctcaaaaggtctggaatgttaagtgttcatttgtctgttgttcatgcttttgatctga---ttttctattc------tccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT
     |  | |       | || |    |     | | | |  | |||| | ||     ||  ||  |||||||||| |||||||   || ||  |||      | ||||||||||| |||||||| |||||||  ||||| ||||||||||||||||| || |||||||  ||||||||||||||||| || 
---taacttgtttgaggctggattttttttgtttgctttcgtgtattaactatt-----gttcgtaattcatgcttt-gatctgaaacttgtcacttcgacacttgcagTTCACAAGGTCAGGCCACACTCAACTCCCTAGTAATGCTATCATGATCACTAGTACAATCACTGTTGTTCTTTTCAGCACGATG

upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 13
-------tgcctatatatgcctcaatagactggcctcaaaaggtctggaatgttaagtgttcatttgtctgttgttc-atgcttttgat-ctgattttctattc---tccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT
          | ||   ||  |        || | |    |    || | | | |     |  ||    | |      |||||||  |  |||||  |||   |   | |||||||| |  || || || |||  || |   |||||||| ||||||||||||||||| ||||  ||||| |||||||||||| | 
gtaggagcaacaatgc-tgattatgggttttgtcttttggaaaattgaattatcagtcactggttcagttataaccagatgctttaaaaactgatactcttaacaaatgcagTTCACCATGTCGGGGCACACTTCACTAAGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTG

upper sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 13
---tgcctatatatgcct-caatagactggcctcaaaaggtctggaatgttaagtgttcattt--gtctgttgttcatgcttttga----tctgattttctattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT
    |   |   ||||     |  |  || | |    |    || | | ||      | ||||  ||       | |||||||  |    |||  | ||      | |||||||| |  || || || |||  ||  |  |||||||| ||||||||||||||||| ||||  ||||| |||||||||||| | 
gtaggatcaacaatgctgattacgggttgtcttttggaaaattgaattattggccactgatttcagttaaaacctgatgctttaaaaacttctactcttaacaaatgcagTTCACCATGTCGGGGCACACTTCACTGCGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTG

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|87152007|gb|DY396796.1|DY396796
EST:     GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG        
genomic: GGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagT
EST: gi|19058280|gb|BM736947.1|BM736947
EST:     GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTCCAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|110481107|gb|EE010953.1|EE010953
EST:     GGGCGGGTTTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|76931825|gb|DV172864.1|DV172864
EST:     GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|76921050|gb|DV168432.1|DV168432
EST:     GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|211218746|gb|FL457360.1|FL457360
EST:     TATTGCGTTGGCTTACAATAAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCAC
genomic: TATTGCGTTGGCTTACAAT-AAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCAC
EST: gi|20300776|gb|BQ163719.1|BQ163719
EST:     GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|18964390|gb|BM660978.1|BM660978
EST:     GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|7216796|gb|AW562918.1|AW562918
EST:     TCTATTGCGTTGGCTTACAATAAG                         TTCGCAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: TCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|149058821|gb|EE156842.2|EE156842
EST:     TCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: TCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
EST: gi|78119305|gb|DV537689.1|DV537689
EST:     GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG                         TTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA
genomic: GGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAGgtaaatcttg ... tattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagtgttcatttgtctgttgttcatgcttttgatctgattttctattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT
                                  atctgat  putative branch site (score: 4)
                                        ttttctattctcc  CT-rich tract
                                       attttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcctatatatgcctcaatagactggcctcaaaaggtctggaatgttaagtgttcatttgtctgttgttcatgcttttgatctgattttctattctccagTTCACAAGATCAGGCCATACTCAACAACCTAGCAATGCTATCATGATCACAAGCACAATCAGCGTTGTTCTTTTCAGCACAATT

- - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatctg