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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggtgccctgccattgtgctgctgcttaaatgagcatatggatattgagcttatgattttccaaaataacttgtgtttgcag

Basic information

species Zea mays
transcript GRMZM2G175419_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G33260.1 (Glycine max), 5'ss of exon 4
GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgta--agttggtgccctgcca---ttgtgctgctgcttaaatgagcatatggatattgagcttatgattttccaaaataacttgtgtttgcag----------------------------------------
|| || ||||| || || |||||||||||||||   || ||| | |||||  |||| || |||||||| || |||||||| |||||||| |||||||||  |     |    | | |   || || |  |  |  |||     ||     | |  |    || ||||   | || | |||  |||                                            
GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACTTGGATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaacactttaatacaagttttatgatattattacaatagttgtacatggacttgggaactgtttttgttagattatttgcattttatatttttgtattgttgtctgatcatcacttgtttttaatcag

upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G35980.3 (Glycine max), 5'ss of exon 4
GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagt--tggtgccctgcca---ttgtgctgctgcttaaatgagcatatggatattgagcttatgattttccaaaat--aacttgtgtttgcag---------------------------------------
|| || ||||| || || |||||||||||||||   || ||||| |||||  |||| || |||||||| || |||||||| |||||||| ||||||||| |      | || | | |   || || |  |  |  |||     ||   | | |  |    || ||||   | ||  ||  ||   ||  |                                        
GATTTTAGTGATCCTCGAGATGCTGATGATGCAAGATATAACCTGGATGGTCGGGATGTTGATGGAAGTCGGATTATTGTGGAATTTGCAAAAGGGgtaggaaacatttccatacaagttttatgatatttttacaatagttgtacatagacttgggcactgtttttggtagatttaatctgcactttaatatttgtatttttgtctgatgttcacttgtttttaatcag

upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 5'ss of exon 2
GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttg-gtgccctgccattgtgctgctgcttaaat----gagcatatggatattgagcttatgattttccaaaataacttgtgtttgcag-------
||||||||||| ||||| |||||||||||||||   || ||| || ||||  | ||  | |||||||| || || ||||| |||||||| |||||||||||||| |||  ||  |||  |     ||  |||||    || ||| |  || |||    ||||    ||  ||  || | |   | |  |       
GAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGGgtaagttgtgtgaactttcatactttctgtgactaaatttgagaacatgtttatgttggaagtatgcaactcttaaccaaatggctctggatgaatgctt

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|37421775|gb|CF648589.1|CF648589
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|78109291|gb|DV527707.1|DV527707
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|15208745|gb|BI430629.1|BI430629
EST:     ATGGCAGGGAAGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGAATACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|31360494|gb|CD444851.1|CD444851
EST:     GCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTAC-ACGGAAGAGGACCTCCA
genomic: GCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|21809627|gb|BQ667945.1|BQ667945
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|76290330|gb|DV029898.1|DV029898
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|61118470|gb|DN559431.1|DN559431
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|32795893|gb|CD948129.1|CD948129
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|60354503|gb|DN221476.1|DN221476
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
EST: gi|94473189|gb|EB702147.1|EB702147
EST:     ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGG                         GTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA
genomic: ATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggt ... gtgtttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGATTACAACGGAAGAGGACCTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTCAGTGACCCCCGTGATGCTGATGATGCACAGTACAACCTAGATGGCAGGGACGTCGATGGAAGCCGCATTATTGTTGAATTTGCTAAAGGGgtaagttggtgccctgccattgtgctgctgcttaaatgagcatatggatattgagcttatgattttccaaaataacttgtgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG