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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggtcctttcttgctactagtactatctactttttgggattaattcatgcatattgtttgtttttgtagtatctggctatctgctaatatttcttctatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATACTTTATTTGCCAGTGGACCTCCAACACTTCCCAGTGCTCCTCAGGCTAA

Basic information

species Glycine max
transcript GLYMA12G36950.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 8
gtgaggtcctttcttgctactagtactatctactttttgggattaat-tcatgcatattgtttgtttttgt-agtatctggctatctgctaatatttcttctatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATACTTTATTTGCCAGTGGACCTCCAACACTTCCCAGTGCTCCTCAGGCTAA
     | ||    |||  |   |  |   || ||||| |  |||| | |  |     |    | |||| |  |  || ||  ||| ||||         || |   ||||||||| |||||||||||||| ||||||| | | |  ||||||||||| || || || ||||| ||||||||||| |||||||||| || ||||||||| ||
----tgaccagagttgacatctgcccctgctgcttttagttattattattttttgagtcaaatattttagagaacatttgcttatttgctg-------ctcgaccatgcagAAAGGGTTTTGGCTGCAAGCAATCCAAGTGCTCCAAAGAGCAGGCCCCACACCTTGTTTGCGAGTGGACCTCCTACACTTCCCAATGTTCCTCAGGCCAA
















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|208085064|gb|GD883614.1|GD883614
EST:     AGACACTAAGGGTGAACGGTCATGGTACCCCAGTCTAG                         AAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCAT
genomic: AGACACTAAGGGTGAACGG-CATGGTACCCCAG-C-AGgtgaggtcct ... tatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCAT
EST: gi|208219432|gb|GE018780.1|GE018780
EST:     AGACACTAAGGGTGAACGGCATGGTACCCCAGCAG                         AAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATA
genomic: AGACACTAAGGGTGAACGGCATGGTACCCCAGCAGgtgaggtcct ... tatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATA
EST: gi|208223041|gb|GE021738.1|GE021738
EST:     AGACACTAAGGGTGAACGGCATGGTACCCCAGCAG                         AAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATA
genomic: AGACACTAAGGGTGAACGGCATGGTACCCCAGCAGgtgaggtcct ... tatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATA
EST: gi|193716934|gb|FK649872.1|FK649872
EST:     ATATGCTTATAAGAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAG                         AAAGAGTTTTGGCTGC
genomic: ATATGCTTATAAGAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAGgtgaggtcct ... tatggtgcagAAAGAGTTTTGGCTGC
EST: gi|193459950|gb|FK428735.1|FK428735
EST:     GAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAG                         AAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATA
genomic: GAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAGgtgaggtcct ... tatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATA
EST: gi|193644982|gb|FK588802.1|FK588802
EST:     ATATGCTTATAAGAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAG                         AAAGNGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCA
genomic: ATATGCTTATAAGAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAGgtgaggtcct ... tatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtttgtttttgtagtatctggctatctgctaatatttcttctatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATACTTTATTTGCCAGTGGACCTCCAACACTTCCCAGTGCTCCTCAGGCTAA
                              tgctaat  putative branch site (score: 2)
                                    tatttcttct  CT-rich tract
                                 taatatttcttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggtcctttcttgctactagtactatctactttttgggattaattcatgcatattgtttgtttttgtagtatctggctatctgctaatatttcttctatggtgcagAAAGAGTTTTGGCTGCAAGTAATCCAACTACACAGAAGAGCAGGCCTCATACTTTATTTGCCAGTGGACCTCCAACACTTCCCAGTGCTCCTCAGGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC