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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtattttttcagcattgttctagtcaaagcttctgatatcctgcttcctttggcctttttaaaacatgtag

Basic information

species Glycine max
transcript GLYMA12G08330.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 5'ss of exon 17
--------------------------------ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaa---gttgagaaatttg-tattttttcagcattgttc--------tagtcaaagcttctgatatcctgc-ttcctttggcctttttaaaacatgtag
                                |||| |||||||| ||||| ||||| ||||| ||||||||  | |||||||||||||||||| | || ||||   |||  | |  ||| | |||| | |    |||||        || |   |  |||  |||       ||   ||    |||  |||| | | ||
TGGCTGCTCCATCATTAGCTGCTCATTCTCAGATGATAATAATGTTTATTATTGTGTGGGAACAGCATATGTTTTACCAGAGGAAAATGAACCATCAAAGgtaatatgtttggtagcttgatgttttcttacaggtgttcgatctcattaatagtattttcaaataaaaaaagttgtatttttgtttgaaaaataggaag

upper sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G430027_T01 (Zea mays), 5'ss of exon 5
--------------------------------ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgag-aaatttgtattttttcagcattgttctagtcaaa--gcttctgatatcctgcttcctttg--gcctttttaaaacatgtag-----------------------------------------------------------
                                ||||||||||||| ||||||||||| ||||||||||||||  | || || ||||||||||||||||| || |  |     || |  |  | ||| |  | ||  ||||| ||   | || | ||| | || |   |||   || | ||| |   |  |                                                             
TGGCTGCTCCATCATTAGCTGTTCGTTTGTGGATGACAATAATGTCTATTACTGTGTGGGAACTGCATATGTTATACCTGAAGAAAATGAACCAACCAAGgtgatatatctgaaatcatgatcttttactaatg--ctagttaactcgtttttaata-cttgttcaatttacagcttgttttagttaatttctcagtgagccttttctatttctcgtgcacaaaatggttatgtatcggtacatcttgtag

upper sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G402002_T01 (Zea mays), 5'ss of exon 17
--------------------------------ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagt----tgagaaatttgtattttttcagcatt-----gttctagtcaaagcttctgatatcctgcttcctttggcctttttaaaacatgtag-----------------------------------------------------------------------------------
                                |||| | |||||| ||||||||||| ||||||||||||||  | || || ||||||||||| || || |||  |    ||| |   |  | |||    |  | |     ||||   |  ||    || | || ||| ||   |   || |||||| || |||                                                                                     
TGGCTGCTCCATCATTAGCTGTTCGTTTGCGGATGATAGTAATGTTTATTACTGTGTGGGAACTGCATATGTTATACCTGAAGAAAATGAACCGACGAAGgtagtttatctgaaagcatgatgtttcactaatactagtcagttcccttttaatacgctaaaatactggttaact---cccttttaatacttgtccaatttactgcttgtagtttatttctctgtgaaccttgtctatttctcgtgcacaaaatgcttatgtgttggcacatcttgtag

upper sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 16
--------------------------------ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtattttttcagcattgttctagtcaaagcttctgatatcctgcttcctttgg---cctttttaaaacatgtag-----
                                | || || ||||| |||||||| |||||||| ||||||||  | || ||||||||||||||||| || |||  |        |   |   | ||| || |  ||   |||||  ||||  | |  |   || ||      | | |||  |   |||       
TGGTTGTTCAATTCTGAGCTGCTCATTCACCGAAGATAAAAATGTCTATTACTGCGTTGGAACCGCATATGTTTTACCGGAGGAAAATGAACCAACTAAGgtatctgttttctctgagaacatatcaacact-ctcagttcaaatattcttttctaatttgtctttgaaatacttatttttattttgtgatttag

upper sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 17
--------------------------------ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgta--agttgagaaatttgtattttt-tcagcattgttctagtcaaagcttctgatatcctgcttcctttggcctttttaaaacatgtag
                                | ||||| ||||| ||||| |||||||| || ||||||||  |||| ||||||||||||||||| || |||  | || ||  |     | |  | |     |||||   || |||  ||     ||| |      |||    | |||     ||||||
TGGTTGCTCCATATTGAGCTGCTCGTTTACAGACGACAAAAATGTCTATTATTGTGTTGGTACAGCATATGTTTTGCCCGAGGAAAATGAACCAACTAAGgtatcatttcagtgagactcactactgtttattttgtttgtgtgaaaattt-----atcttttcatttttatattgtttcgtggatgtag

upper sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 17
--------------------------------ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtatttt--ttcagcattgttctagtcaaagcttctgatatcctgcttcctttggcctttttaaaacatgtag-----------
                                |||| | |||||| ||||| || ||||| || ||||||||  | |||||||||||||| |||||||| ||||  ||  | ||| |||  |   | ||    |||     |  |    | || |  |    |  |  | ||  | | ||   ||||             
TGGTTGCTCTATCCTTAGCTGCTCCTTCTCTGATGATAGTAATGTATATTATTGCGTTGGGACCGCATATGTTTTACCAGAGGAAAATGAGCCAACCAAGgtaaaatgccatattagtacatacatacatacctgtatatatgtattggtttgttgccagaatagcacttgcagtctaaattaatgtctgaatcgctgag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACAATAATGTGTATTACTGTGTTGGAACTGCATATGTACTGCCAGAGGAAAATGAACCAACCAAAgtaagttgagaaatttgtattttttcagcattgttctagtcaaagcttctgatatcctgcttcctttggcctttttaaaacatgtag

- - - - - - - - - - - - - - - - - - - - - - - AGAGGA