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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttcccgcgctcttccccaacccttggattgggtgaagacgtgaagtatagaacctacacttttcgttaacttgcaaattt...

Basic information

species Glycine max
transcript GLYMA01G30400.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 12
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaag--tcaagc-tggatatt---------tttcccgcgctcttccccaaccc-ttggattgggtgaagacgtgaagtatagaacctacacttttcgttaacttgcaaattt------------------
||||  ||||||| ||||| || ||||| |||||||||||||| ||||| || |||||||||||  || ||||||| ||||||||||| ||| | |||||||| |  || ||| || | ||          ||| | |   | | | | ||     |||||      | |  ||| |   | || | |  |  ||| |  ||  | |  ||||                  
TCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAGTATCTCTACAAgtatgtatctagcatgcaaatccatagtcagtttacagttgtttgctcgaataagctggatatatccatgtggtggatattggagcatcaaacttttgaaaatgttctgattttaacatctgaatatgcag

upper sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttcccgcgctcttccccaaccct-tggattgggtgaagac-gtgaagtatagaacctacacttttcgttaacttgcaaattt----
||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||| ||| |||| |||||||||||||| ||| | ||||||| ||||   |   ||      |        || | |     |   | |   ||  | |   | || | | ||   ||  ||  || || ||    |||  |    
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctc-ccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaatttcgactgtattctgatcctttaccacaaaacatgcag

upper sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM5G871262_T01 (Zea mays), 5'ss of exon 1
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtca-agctggatatttttcccgcgctcttccccaacccttggattgg-gtgaagacgtgaagtatagaacctacacttttcgttaacttgcaaattt-----
||||  |||| || |||||||| ||||| ||||||||||| || || || || ||||||||||| ||| |||| |||||||||||||| ||| | ||||||| ||||  |  || | | |           |||     ||   |  ||||  ||| | |  | ||   | |||| |||  |  |  || |    ||||        
TCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctcaaatgaagagtgaaattagttgctttgtttacaggt--attgctgtggatatttaaaactt-gaacgtactttgatacttgaaccacaaaacatgcag

upper sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 12
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 5'ss of exon 12
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttcccgcgctcttccccaacccttggattgggtgaagacgtgaagtatagaacctacacttttcgttaacttgcaaattt
||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||||||||| ||| | || ||||| || ||||| ||  | ||||||||||| |    || | |||| |         || |  ||   || |       |||||      ||     ||    ||| ||| || ||| ||     
TCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAGTACCTCTACAAgtaagtaatatcgggt-ttttgcaaataaaggtctc--acttgtgtacat----aagactgatgataatcttccctttcttatcggtatctttcag----

upper sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 12
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttcccgcgctcttccccaacccttggattgggtgaa-gacgtgaagtatagaacctacacttttcgttaacttgcaaattt
||||| ||||||||||||  |||||||||||||||||||| |||||||||||||||||||||||  ||||||||||    |||||||||||||| |||||||  || |        ||| |||  |   ||| |      |||  ||||||    | |      | |        ||  |   | ||| |  ||||     
TCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAATATTTATACAAgtcggtaaca------attgttcatg---tctactgatgtcctctgattggagatatggtactgatttggttgtgtatgcccattgttgaactgcag----

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|15663627|gb|BI700998.1|BI700998
EST:     ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|16344579|gb|BI970174.1|BI970174
EST:     ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|21479814|gb|BQ576497.1|BQ576497
EST:     TGGAATCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
genomic: TGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|16345834|gb|BI971429.1|BI971429
EST:     ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|14991711|gb|BI317384.1|BI317384
EST:     ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|209716276|gb|BW657579.1|BW657579
EST:     GAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
genomic: GAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
EST: gi|17022512|gb|BM093546.1|BM093546
EST:     ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAA                         GTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT
genomic: ATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaag ... cacatcacagGTACAACGTCTTTCAGATTGCATTTGTTGCATTGGCTGGATTGACTTTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttcccgcgctcttccccaacccttggattgggtgaagacgtgaagtatagaacctacacttttcgttaacttgcaaattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccgcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgggtg