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

...tcaatgtattctaacatgccgaatcacatttgagtttatgatttgtgttgaatgttgctttatatatgcttacgtgcacagaaatggaatttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGT

Basic information

species Glycine max
transcript GLYMA16G25200.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25200.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g02010.t01 (Vitis vinifera), 3'ss of exon 2
----------------------tcaatgtattctaacatgccgaatcacatttgagtttatgatttgtgttgaatgttgctttatatatgcttacgtgcacagaaatggaatttgggtt-----cagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGT
                       |||  |    ||||     ||   |  | ||  || |||| |    ||  ||   | | | |     ||||  || |      | |||||  | ||     ||||  | || ||||| || | |||||| || || || |||| |||||||||| | ||||| ||||||||||||||||  ||||||||||| | ||| |||||
gtcattatttggtttttctgttgcaacctgagataactattggaggaatctatgctttcatgaatgaaattagataacgttatgtgctcacttaaatggaacttgtttgaattctgtttttcttcagGGCTGGAGAGATTACCATTCAAGCCAGAGGGTTATAATTTTTGGACATGGCGAGGTCACAAAATACATTATGTAGAACAAGGAGAAGGATTTCCGATTGT
















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|213604690|gb|DB960469.1|DB960469
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|209728317|gb|BW658529.1|BW658529
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|209725699|gb|BW663190.1|BW663190
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|192301616|gb|FG998468.1|FG998468
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|18692833|gb|BM521681.1|BM521681
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|151399533|gb|EV269404.1|EV269404
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|213591367|gb|DB955715.1|DB955715
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|20448288|gb|BQ252412.1|BQ252412
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|13125828|gb|BG316398.1|BG316398
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|151405996|gb|EV275811.1|EV275811
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|120529684|gb|EH257818.1|EH257818
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|20814627|gb|BQ299105.1|BQ299105
EST:     TTCGGTCTCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
EST: gi|209716247|gb|BW657550.1|BW657550
EST:     TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAG                         GTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA
genomic: TTCGGTCGCGGCTTCTACTCTCACAGCCGAAGCAGAACCATCTTCCAAAGgttagtgact ... ttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgaatgttgctttatatatgcttacgtgcacagaaatggaatttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGT
                     tgcttac  putative branch site (score: 2)
             tttatatatgctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatgtattctaacatgccgaatcacatttgagtttatgatttgtgttgaatgttgctttatatatgcttacgtgcacagaaatggaatttgggttcagGTTTTGAAAGATTGCCGTACAAGCCGGAAGGGTACAATTATTGGACATGGAGGGGTCATAAAATACATTATGTAGTGCAAGGAGAAGGCTCTCCCATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA