Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgcaataaaatattttgatttatttacttctagaaattataatcctttgcctttggatgttgaatttaactatatttgctttctttttgtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG

Basic information

species Glycine max
transcript GLYMA13G36230.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
--agtgcaataaaatattttgatttatttacttctagaaattataatcctttgcctttggatgttgaatttaactatatttgctttctttttgtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG
    |   | |   ||| |  | |   || ||  |  |   ||||   || || ||    || |  |  ||   | |  |    || | |   |||   ||| |||||||| || ||||||||||||||||| || || ||||||||||||||||||||  |    |||| |||    || |||
tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctcta--ttgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG

upper sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 12
---agtgcaataaaatat-tttgatttatttacttctagaaattataatcctttgcctttggatgttgaatttaactatatttgctttctttttgtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG
   | |    |  | | | |||  ||||        |  |  || ||  | |  |          || ||    | ||||  |  |  |   || |  |||||| |||||||| ||||| ||||||||||| ||||| || |||||||||||||| |||||||| || |||| |||||| ||||||
tacacttgggtgcattgtcttttgtttaaaattccatgcagtttgtatacttcagttcacaaggattcaa---gattataaattgtcacccgtt-tccttttagGTCTGTGGGCAAAACACAGATGAATGAGCAATCATCCAGAAGTCATTTTGTGTTCACTCTGCGGATATCTGGTGTTAATGAG
















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|193326635|gb|FK288582.1|FK288582
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208139518|gb|GD937276.1|GD937276
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208088757|gb|GD891199.1|GD891199
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTG-
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208278560|gb|GE075805.1|GE075805
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208325770|gb|GE124506.1|GE124506
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACGATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208270354|gb|GE067344.1|GE067344
EST:     AGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: AGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|193508563|gb|FK465426.1|FK465426
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208112030|gb|GD912422.1|GD912422
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208223822|gb|GE020951.1|GE020951
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208232837|gb|GE035362.1|GE035362
EST:     CTTTTAAATCAAGCTGCAAATAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208192985|gb|GD991156.1|GD991156
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208034047|gb|GD831479.1|GD831479
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|193594056|gb|FK548090.1|FK548090
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCCTNTAGAAGTCATTTTG-
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|193686753|gb|FK626118.1|FK626118
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGACATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|193306454|gb|FK273379.1|FK273379
EST:     CATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|207733080|gb|GD710932.1|GD710932
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|207685304|gb|GD668650.1|GD668650
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTT-AAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAA-CTCAGATGAATGAACAATCTTCTAGAAGTCATTT-GT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208117539|gb|GD917781.1|GD917781
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
EST: gi|208045340|gb|GD841134.1|GD841134
EST:     CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAG                         ATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT
genomic: CAGAGTGTAAAAGAGGTTGCATTTCTTTTAAATCAAGCTGCAAGTAGCAGgtaattagtt ... gtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttgcctttggatgttgaatttaactatatttgctttctttttgtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG
                    atttaac  putative branch site (score: 3)
                          ctatatttgctttctt  CT-rich tract
                   aatttaactatatttg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgcaataaaatattttgatttatttacttctagaaattataatcctttgcctttggatgttgaatttaactatatttgctttctttttgtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT