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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgaatctttgattttacacaatttcacttttaactttgcctactcatttcttcttattttattgacatgaatgtgctgtgattttgtttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGTCTTCTTGTTTTATATTTGGGCAAGGCTGAAGCAAGGGACAAAATATGCA

Basic information

species Glycine max
transcript GLYMA09G40060.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40060.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g01890.t01 (Vitis vinifera), 3'ss of exon 1
---atatgaatctttgattttacacaatttcacttt-taactttgcctactcatttcttc-ttattttattgacatgaatgtgctgtgattttgtttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGTCTTCTTGTTTTATATTTGGGCAAGGCTGAAGCAAGGGACAAAATATGCA
   | |||  | |||  |||     ||| | || || |||| |       | |||| ||   | || | |||| ||||| |     || |||   ||    |  |   ||||  || ||||||||||| |||||||||||  | || ||||| |||||| |  |||| ||||||  ||| |||||||| |||||||| ||||   
tctacatgtgtattttgttt-gtttaatgtgacattataacctcattatgttatttttttgcttttctcttgaaatgaaggc-tgatgttttgacttagcagGTGAATTTAGGTTAAAAGATGAGTACTCTGGATGCAACTCGAGCAGAACTCGGTCTTGTAATTTTGTATTTGAACAAAGCTGAAGCTAGGGACAAGATAT---
















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|298179034|gb|HO024769.1|HO024769
EST:     TTCTCCACCACTATTCCCTTCACCCCGATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|192323627|gb|FK019038.1|FK019038
EST:     CTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|213589574|gb|DB973217.1|DB973217
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|151394416|gb|EV264287.1|EV264287
EST:     ACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: ACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|213617944|gb|DB967306.1|DB967306
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|120492016|gb|EH220183.1|EH220183
EST:     CCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: CCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|7686223|gb|AW756934.1|AW756934
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|19348498|gb|BM893030.1|BM893030
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|21888536|gb|BQ741749.1|BQ741749
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|254336245|gb|GR842424.1|GR842424
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|12773457|gb|BG238384.1|BG238384
EST:     CCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAATATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: CCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|23729522|gb|BU762853.1|BU762853
EST:     ATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: ATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|19348375|gb|BM892907.1|BM892907
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|14259242|gb|BG882150.1|BG882150
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCC----------G                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|254335608|gb|GR847136.1|GR847136
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|23057464|gb|BU578138.1|BU578138
EST:     CCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: CCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
EST: gi|213607370|gb|DB967079.1|DB967079
EST:     TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTG                         CTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT
genomic: TTCTCCACCACTATTCCCTTCACCCCAATCACACTTTCCGGTAGTTGTTGgtactctctc ... ttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatttcttcttattttattgacatgaatgtgctgtgattttgtttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGTCTTCTTGTTTTATATTTGGGCAAGGCTGAAGCAAGGGACAAAATATGCA
                 tattgac  putative branch site (score: 2)
                                       ttttgtttc  putative PPT
     ttcttcttattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgaatctttgattttacacaatttcacttttaactttgcctactcatttcttcttattttattgacatgaatgtgctgtgattttgtttcatggcagCTATTAGTGTAGAAGATGAGTACGCTGGATGCAACAAGGGCTGAACTTGGTCTTCTTGTTTTATATTTGGGCAAGGCTGAAGCAAGGGACAAAATATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG