Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatatgtgccaaatgtcatcttctttccagtactttgttggccatttgttaccctgaaggaaaaagacaacccttaaactgaagccgttaatttttattttaaaagaagccattgactttttggcatttgctctctctcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAAACTGGAACCTTCACTATGGATAAGAAGAAGCTACTTCAGCTAGTTGGGA

Basic information

species Glycine max
transcript GLYMA01G06630.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G06630.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0010g00520.t01 (Vitis vinifera), 3'ss of exon 4
gttaatatgtgccaaatgtcatcttctttccagtactttgttggccatttgttaccctgaaggaaaaagacaacccttaaactgaagccgttaatttttattttaaaagaagccattgactttttggcatttgctctctctcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAAACTGGAACCTTCACTATGGATAAGAAGAAGCTACTTCAGCTAGTTGGGA
                                                 | ||  | ||||  || | | ||     |||  |        |     | | ||  ||       | | |    |    || | ||| || ||    |||| |||||||| | |||||||| ||| | |  |||||||| |||||||||||||||||||| ||||| ||||||| || ||||||  | || || ||||| |
-------------------------------------------------tattttcttgaaacaacatgcca-tttataatgtagttttagtggaactaaattcgaatttttttaataatcaatattaatattctccctttctccctcagATTGATGGTATGGTTGAAGAATTTACAGATATAAATCGTGGAATGGAGAAAACTGGAACTTTCACAATGGATAGGAGGAAGCTCTTCCAACTTGTTGGAA
















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|193646921|gb|FK589194.1|FK589194
EST:     TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAG                         GTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAACCGCGGAATGGAGAAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
EST: gi|18848595|gb|BM567752.1|BM567752
EST:     TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAG                         GTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
EST: gi|193593283|gb|FK545801.1|FK545801
EST:     TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAG                         GTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAACCGCGGAATGGAGAAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
EST: gi|192321870|gb|FK013234.1|FK013234
EST:     TTGGAAGTGTATTGGGACAA-GCATAGCTCTGGATTATTT-GTCTCACAG                         -TTGATGGTTTAGTTGAAGAGTTTGCTGGCATAA-TCGCGGA-TGGAGAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAA
EST: gi|254324255|gb|GR840572.1|GR840572
EST:     TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAG                         GTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATG-AGAAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
EST: gi|254324256|gb|GR840573.1|GR840573
EST:     TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAG                         GTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
EST: gi|192321869|gb|FK013233.1|FK013233
EST:     TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAG                         GTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
EST: gi|22930913|gb|BU548052.1|BU548052
EST:     NNNGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAG                         GTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA
genomic: TTGGAAGTGTATTGGGACAAAGCATAGCTCTGGATTATTTTGTCTCACAGgttaatatgt ... tcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattttaaaagaagccattgactttttggcatttgctctctctcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAAACTGGAACCTTCACTATGGATAAGAAGAAGCTACTTCAGCTAGTTGGGA
                  cattgac  putative branch site (score: 3)
                                  tttgctctctctcatt  putative PPT
     ttttaaaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatatgtgccaaatgtcatcttctttccagtactttgttggccatttgttaccctgaaggaaaaagacaacccttaaactgaagccgttaatttttattttaaaagaagccattgactttttggcatttgctctctctcattatcagGTTGATGGTTTAGTTGAAGAGTTTGCTGGCATAAATCGCGGAATGGAGAAAACTGGAACCTTCACTATGGATAAGAAGAAGCTACTTCAGCTAGTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT