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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatgacctataacagattgatgccttttacaatgtaaacggtgttcttcaacaccaatgtatatatgcctcaccctgtcaaatgattgtaacgcag

Basic information

species Glycine max
transcript GLYMA06G02200.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 4
ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatgacctataacagattgatgccttttacaatgtaaacggtgtt-cttcaacaccaatgtatatatgcctcaccctgtcaaatgattgta-acgcag
||| || ||||| || |||||||| ||||||||||||||||| || || || |||||||| ||||||||||||||||||||||| |||||||| || ||||||   ||    ||||||| ||   |  |  |  |  | | |||   | || |   |  | ||  || | |     | | |     || |    ||  |  |  
ACGTGTTGCAAGACAAATGGTTGAAAGATTTGGATTCAGCAAGAAGATCGGGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatca----ctataactgaaatagactatcaaagaagaaaaacttcttaccctagaagcagagtctgtgaaaattaactgaagaactagacgtgcaaactt

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G126361_T03 (Zea mays), 5'ss of exon 5
ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatgac--ctataacagattgatgccttttacaatgtaaacggtgttcttcaacaccaatgta-tatatgcctcaccctgtcaaatgattgtaacgcag
||| || |||||||||||||| || |||||||||||||| || || || || |||||||| || || ||||| |||||||| || |||||||| ||||||||||||        ||  ||  |||    ||||   |  | | | |   |     | |      | | | ||      | | | |    |||| ||||       
ACGTGTCGCAAGGCAGATGGTCGAAAGATTTGGATTCAGTAAGAAGATCGGCCAAGTTGCGATCGGGGGACCGGGTGGAAACCCTTTCTTGGGGCAACAGgtatgctgctgtaactgaaatggatgttagcctggaattaggaacatactaaaactaagtgaagaagaactaggcatgtaaacttcaacaatggttgtct-----

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 4
ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgc-catgacctataacagattgatgccttttacaatgtaaacggtgttcttcaacac-caatgtatatatgcctcaccctgtcaaatgattgtaacgcag
 || |||||  | || |||||||||||||| || ||||||||||| ||||||||||||||  |||||||| | || ||||| || ||||||||||||   ||| |   || |      | |    | |   ||| | ||| ||    ||  | | || | | |||   || | |   |  |                       
GCGGGTGGCTCGCCAAATGGTTGAGAGATTCGGGTTCAGCAAAAAGATTGGACAAGTTGCAGTTGGTGGAGCAGGAGGAAACCCTTTCTTGGGTCAAAGTgtaagtatataaaactcgatactcaggt---tttcataatttattgtgttgtttccagctctcaaaacatgttttgtttgcag---------------------

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 5'ss of exon 4
ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatgacctataacagattgatgccttttacaatgtaaacggtgttcttcaacaccaatgtatatatgcctcaccctgtcaaatgattgtaacgcag
 || |||||| | || ||| ||||||||||||| ||||||||||| ||||||||||||||  ||||||| |||||||||||||| ||| |||||||||| ||||        || |  | | || ||   |       |     ||      |  |     | | |||||||  |       || ||||| || |   |   
TCGTGTGGCACGTCAAATGATTGAGAGATTTGGGTTCAGCAAAAAGATTGGACAAGTTGCTGTTGGTGGCCCTGGTGGAAATCCCTTCATGGGTCAACAAgtatattg----ctttctcggtttcatcattagggttgttggttcgacaagttggagtgttact-tatatatatcc------gtgaaatgtttttgcag---

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 4
ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgc-catgacctataacagattgatgccttttacaatgtaaacg-gtgttcttcaacaccaatgtatatatgcctcaccctgtcaaatgattgtaacg-cag
||| ||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||| |  |||    ||  | |  ||| |  |    |   || |  |   ||   |||| ||||    |    | |  | | | | |    || ||  || | |||
ACGGGTGGCCAGGCAGATGGTGGAGAGATTTGGGTTCAGCAAAAAGATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTAGGTCAACAGgtaggaacatattttaagatattttgctctccccaagtgtggagtcccatgcgattcatcacc----ttaccaagattgaacatttttggtgtttcaaatggcag

upper sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ31931 (Selaginella moellendorffii), 5'ss of exon 4
ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatgacctataacagattgatgccttttacaatgtaaacggtgttcttcaacaccaatgtatatatgcctcaccctgtcaaatgattgtaacgcag
 ||||| ||| | |||||||| ||| |||||||||||||||| || ||||| || || ||  | |||||  ||||||||||||| ||| | || ||||||||    | ||  | | | ||||   |        | | |  |||| |     | |     |  | | | | | | || |                       
GCGAGTTGCACGCCAGATGGTGGAGCGATTTGGATTCAGCAACAAGATTGGCCAGGTCGCTCTCGGTGGCTCTGGTGGAAATCCTTTCCTCGGCCAACAGgt---tcttgcgcaaaatcagaaaca--------aaagtagaaactgaaacttactctctctttttctttgttcttcgcag---------------------

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|209716217|gb|BW654265.1|BW654265
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|213601060|gb|DB983735.1|DB983735
EST:     GAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGTTTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|17962858|gb|BM269614.1|BM269614
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|151405829|gb|EV275644.1|EV275644
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|209718945|gb|BW674798.1|BW674798
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|192314907|gb|FK010725.1|FK010725
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGGAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|151393635|gb|EV263510.1|EV263510
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|151401015|gb|EV270829.1|EV270829
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|20811366|gb|BQ295844.1|BQ295844
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|209729428|gb|BW663689.1|BW663689
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|209710311|gb|BW676375.1|BW676375
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
EST: gi|209701415|gb|BW667316.1|BW667316
EST:     GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAG                         ATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG
genomic: GACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatg ... tgtaacgcagATGTCATCGCAAAAGGATTACTCCATGGCAACTGCGGATGTAGTGGATGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGAGTGGCAAGGCAGATGGTTGAGAGATTTGGATTCAGCAAAAAAATTGGACAAGTTGCCATTGGTGGACCTGGTGGAAATCCATTCTTGGGTCAACAGgtatgccatgacctataacagattgatgccttttacaatgtaaacggtgttcttcaacaccaatgtatatatgcctcaccctgtcaaatgattgtaacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA