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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagaacatactctacaaagtggcgtaaactatttaacttgcctcttatggtccttgaattatagaattgttgaattaacggaactgttttaaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG

Basic information

species Zea mays
transcript GRMZM2G046587_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------tgagaacatactctacaaagtg-gcgtaaactatttaacttgcctcttatggtccttgaattatagaattgttgaattaacggaactgttttaaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG
                                             | |  | || | | |     |   || || ||        ||||  |   |  |     |  | |   |  | | ||||  |    |  | | | | |        ||||||| |||||| ||||| ||||||||||||||||| || ||||||||                                
ttttttaacctgtttttacagagtatcttgtttgcttgccatatccttgatttagataatacattttggcttttcaatgacatatttataatttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCAC-TGGGATCAAGATACCCCCCTGCTGCTCTCAACGAGCGCATCCTTTCTTCCATGTCTCAAAAACATGT--------------------------------
















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|211537734|gb|FL105292.1|FL105292
EST:     CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCG                         CCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
genomic: CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCGgtgagtggcg ... taaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
EST: gi|88756535|gb|DY540676.1|DY540676
EST:     CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCG                         CCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
genomic: CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCGgtgagtggcg ... taaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
EST: gi|13126709|gb|BG317279.1|BG317279
EST:     GCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGACTCCG                         CCATGGCTGGANCCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTC
genomic: GCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCG-CTCCGgtgagtggcg ... taaatcgtagCCATGGCTGGA-CCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTC
EST: gi|13126289|gb|BG316859.1|BG316859
EST:     CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCG                         CCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
genomic: CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCGgtgagtggcg ... taaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
EST: gi|13491080|gb|BG517844.1|BG517844
EST:     CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCG                         CCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
genomic: CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCGgtgagtggcg ... taaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
EST: gi|149099849|gb|EE185901.2|EE185901
EST:     CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCG                         CCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC
genomic: CGCACTCGCCTGTCGCCTCTTCTCGCTTTCGCCACCGGGGCAGCGCTCCGgtgagtggcg ... taaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggtccttgaattatagaattgttgaattaacggaactgttttaaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG
                            aattaac  putative branch site (score: 2)
                                       ctgtttt  putative PPT
            aattatagaattgttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagaacatactctacaaagtggcgtaaactatttaacttgcctcttatggtccttgaattatagaattgttgaattaacggaactgttttaaatcgtagCCATGGCTGGACCTGCTGTTCTCAATGAGCGTATCCTTTCTTCCATGTCCCAGAAACATGTTGCTGCTCACCCATGGCATGATTTGGAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- -gaacata
- - - - - - ctacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - gtccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttt