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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtggacttacctcttggaattccttgccaatcaaaaggaatgtgatctgcatttattaattaagggagagttctggacaatactactgtcctt...

Basic information

species Zea mays
transcript GRMZM2G154165_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA16G08410.1 (Glycine max), 5'ss of exon 19
GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtggacttacctcttggaattccttgccaatcaaaaggaatgtgatctgcatttattaattaagggagagttctgga-----caatactactgtcctt-------------------------------------------
| ||  ||||||| || ||||||||||| ||||||||||| ||||||||||| || ||||| |||||||||||||| ||||||||| |||||||  | |||||||    |  ||      |   |||  ||    |  |  |   ||  || |   |||    |  |   || | |  ||       || || || |   |||                                           
GACTGGTTGGCTATCCCAGTGATGATATCAATAAGTTCCTGTGGATGGTTCGTATTGGAGGGGGTGTATTCCCTCACATAAAGGAACCAGATTATTTAgtaagttaaacaagtaatatgggttgttcaatgttttttcatggctttgatattttattttggagaacagatgatactcttgcttccttcagtaataatcagcttttgaggagtgttaacacctttttttttcttcaaattttaaaag

upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA01G01270.1 (Glycine max), 5'ss of exon 19
GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttg-----------tggact---------tacctcttgg--aattccttgccaatcaaaaggaatg-tgatctgcatttattaattaagggagag-ttctggacaatactactgtcctt----------------------
| ||  ||||||| || ||||||||||| ||||||||| | ||||||||||| || ||||| |||||||||||||| ||||||||| |||||||  | |||||||            ||| ||         ||  || ||    ||   ||       | ||   ||| |  |||   ||  || | |||     || || ||   | |  ||    | ||                      
GACTGGTTGGCTATCCCAGTGATGATATCAATAAGTTCTTGTGGATGGTTCGTATTGGAGGGGGTGTATTCCCTCACATAAAGGAACCAGATTATTTAgtaagttaaacgagtaatatgggctgttcaatgttatatcatgactgatattttattttggagaacagatgatactctagcttccttcagtaataatcagcttttgaggagtgttaacacctttttttctcttcaaattttaaaag

upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 17
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 5'ss of exon 19
GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtggacttacctcttggaattccttgccaatcaaaaggaatgtgatctgcatttattaattaagggagagt---tctggacaatactact--gtcctt------------
| |||||||| ||||| |||||||| || || ||||| || ||||||||||| || ||||| || || || || || ||||||||||| ||||| || |||  |  | |  ||   |  |    || ||| |      | |  ||  ||   ||  |  || | ||    ||   |   |||| ||     |||    |  ||            
GTCTTATTGGTTACCCTAGTGATGACATCAACAAGTTTCTGTGGATGGTTCGTATTGGAGGCGGCGTCTTTCCACATATAAAGGAAGCTGATTATCTGgtacttatttgttttgttttgttttgtttctttcggtcttagaacaagttgtgatggctcaataattttgaagactttgaatctgaacctggttacctaatatttgctttgcaaaag

upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 17
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 5'ss of exon 19
GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtggacttacctcttggaattccttgccaatcaaaaggaatgtgatctgcatttattaattaagggagagttctgg--acaatactactgtcctt--------
| ||| |||| || || |||||||| |||||||||||||| ||||||||||| || ||||| || |||||||| || || | |||| | ||||| || || |||||| |      | |||| ||     |    ||   ||| | ||||  ||     |  | |||   || |  || | |  ||| |  |      |||        
GTCTTGTTGGATATCCGAGTGATGACATTAATAAGTTCCTGTGGATGGTTCGCATAGGAGGGGGGGTATTCCCCCACATCAGGGAACCTGATTATCTGgtgagttgttggt----cgcttgtaa-----tatggattctaagta-tgtgtcctttgggttcttattgctggtgtattgttgctacactggtttcaagctttgttccat

upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 17
lower sequence: Vv03s0088g00210.t01 (Vitis vinifera), 5'ss of exon 5
GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtgga---cttacctcttggaat-----------tccttgccaatcaaaagg--aatgtgatctgcatttattaatta-agggagagttctggacaatactactgtcctt-------------------------------------------------------------------------------------
         | || || |||||||| |||||||||||||| ||||||||||| || ||||| || ||||||||||| || |||||| | ||||| || || |||||| |    |||      |||| |           |||||     ||  |  |    |||  | |   |  | || ||  | |    ||||      | | | |     ||                                                                                     
---------GATATCCGAGTGATGACATTAATAAGTTCCTGTGGATGGTTCGCATAGGAGGGGGGGTATTCCCTCACATCAAGGAACCTGATTATCTGGTGAGTTGTTGgttgcttgtaatatggattctaagtatgtctcctttgggttcttattgctggtgtattgttggtacactagtttcaagctttgttccatttgagattccaaatatttgtcttgattggcaatagactaacatttaagttgaatctcacttgatggtctcacattattggtgaatttgcatttggttgaaag

upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 17
lower sequence: Vv11s0016g01590.t01 (Vitis vinifera), 5'ss of exon 3
GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtggacttacctcttggaattccttgccaatcaaaaggaatgtgatctgcatttattaattaagggagagttctgg--acaatactactgtcctt--------
| ||| |||| || || |||||||| |||||||||||||| ||||||||||  || ||||  || ||||||||||| || |||||| | ||||| || || |||||| |  |     |||| ||     |    ||   ||| | |||   ||     |  | |||    | |  || | |  ||| || |      |||        
GTCTTGTTGGATATCCGAGTGATGACATTAATAAGTTCCTGTGGATGGTTCACATAGGAGTGGGGGTATTCCCTCACATCAAGGAACCTGATTATCTGgtgagttgttggttg----cttgtaa-----tatggattctaagta-tgtctcctttgggttcttattgctagtgtattgttgctacactagtttcaagctttgttccat

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|67014712|gb|CO443461.1|CO443461
EST:     TTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT                         AAGGATGGCAACTACCGTGTTGATGCTCATAGTACCCCAACCATGTTGAAT
genomic: TTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtg ... catttcttagAAGGATGGCAACTACCGTGTTGATGCTCATAGTACCCCAACCATGTTGAAT
EST: gi|76017469|gb|DT944639.1|DT944639
EST:     CCTCAAATAAAGGAAGCAGATTACCTT                         AAGGATGGCAACTACCGTGTTGATGCTCATAGTACCCCAACCATGTTGAAT
genomic: CCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtg ... catttcttagAAGGATGGCAACTACCGTGTTGATGCTCATAGTACCCCAACCATGTTGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTTgtaagttgtggacttacctcttggaattccttgccaatcaaaaggaatgtgatctgcatttattaattaagggagagttctggacaatactactgtcctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT