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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatagtaattctaactggtaaatatccatgccctgttttattttccattaagctttctttctttttttgcttactttggttattcatttgccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTTGAGTGAGGGTGAATAACTTTCTGTATAAACAGATGCAACTCTTCAGAAT

Basic information

species Glycine max
transcript GLYMA02G46540.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46540.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00310.t01 (Vitis vinifera), 3'ss of exon 3
-----caatagtaattctaactggtaaatatccatgccctgttttattttccattaagctttctttctttttttgcttactttggttattcatttgccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTTGAGTGAGGGTGAATAACTTT-CTGTATAAACAGATGCAACTCTTCAGAAT-
       ||  | ||| | | | || ||  |  ||||  |        |  ||||| || |  ||| | |  |   |||||    |   |  |   |  | | |||||||| ||||||||||||||||||||||| || ||||| || || ||| | | ||| |  || | |  |   | || ||| || ||||   |   ||| | 
gcattttatttttattttta-tagtgaacttgaatgcagtag---gaatatcattatgcatattttatatggtgatttactaaaatcccttctccact-tgttagGTGGGCAATTGTATATCTGGCACAGATGAACCCACTCATTGTCCCAATCCTCAATGAAGTGGAGTGAGATGATTCTACAAAGAG-TGCA-TGCGGAAGATTG

upper sequence: GLYMA02G46540.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00270.t01 (Vitis vinifera), 3'ss of exon 3
-----caatagtaattctaactggtaaatatccatgccctgttttattttccattaagctttctttctttttttgcttactttggttattcatttgccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTTGAGTGAGGGTGAATAACTTT-CTGTATAAACAGATGCAACTCTTCAGAAT-
        |   |||| | | | || ||  |  ||||  |        |  ||||| || |  ||| | |  |   |||||    |   |  |   |  | | |||||||| ||||||||||||||||||||||| || ||||| || || ||| | | ||| |  || | |  |   | || ||| || ||||   |   ||| | 
tgcattttttaaaattttta-tagtgaacttgaatgcagtag---gaatgtcattatgcatattttatatggtgatttactaaaatcccttctccact-tgttagGTGGGCAATTGTATATCTGGCACAGATGAATCCACTCATTGTCCCAATCCTCAATGAAGTGGAGTGAGATGATTCTACAAAGAG-TGCA-TGCGGAAGATTG
















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|58017908|gb|CX704650.1|CX704650
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacat ... gccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
EST: gi|58024344|gb|CX711085.1|CX711085
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACACCATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacat ... gccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
EST: gi|213605320|gb|DB978766.1|DB978766
EST:     TACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTAACGTC-GGCACAGATGAAACCGCTCATAGTACCTATCT
genomic: TACTGCAACAACATGCTGCTGGATGATgtaagtacat ... gccatatcagGTGGGCGATTGT-ATATCTGGCACAGATGAAACCGCTCATAGTACCTATCT
EST: gi|213611533|gb|DB960813.1|DB960813
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacat ... gccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
EST: gi|151405738|gb|EV275552.1|EV275552
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacat ... gccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
EST: gi|16275913|gb|BI941587.1|BI941587
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacat ... gccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
EST: gi|58021214|gb|CX707956.1|CX707956
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacat ... gccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattaagctttctttctttttttgcttactttggttattcatttgccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTTGAGTGAGGGTGAATAACTTTCTGTATAAACAGATGCAACTCTTCAGAAT
                       tgcttac  putative branch site (score: 2)
         tttctttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatagtaattctaactggtaaatatccatgccctgttttattttccattaagctttctttctttttttgcttactttggttattcatttgccatatcagGTGGGCGATTGTATATCTGGCACAGATGAAACCGCTCATAGTACCTATCTTGAGTGAGGGTGAATAACTTTCTGTATAAACAGATGCAACTCTTCAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG