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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatactttgttctactgggttcttgtcttggtttctctgaattgctttgccatgacttttatgcagtacacatgctaacttttattttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGTTAAATACT

Basic information

species Glycine max
transcript GLYMA06G11850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11850.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g59550.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------tatactttgttctactgggttcttgtcttggtttctctga-attgctttgccatgacttttatgcagtacacatgctaacttttattttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGTTAAATACT
                                                         || | ||  |  |||||  |  |   || | ||| | ||     |  || |||  |   | |  ||    |  |  | || |||  ||   | |   ||||||| |||||||| || ||||||||||| ||||| ||||||||  ||||  | || ||  |||||||||||||    ||  |  ||   |||||  | || 
gtaggtgctcatcttatggcgggtgtaatgactggtgctttacttctgctgtgatcttacagtt-ataatactgtatggtaaactggatttttttgtcgccgtgttaccagcaaagtaaatcatgttattta-tgacgtttccttgtgttttcttcagCATTAACACAGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCTACCAGCAGTGTTACTTGAAGGAGGCGGTGTGGTTACCTGGTTCTACACA

upper sequence: GLYMA06G11850.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g02970.t01 (Vitis vinifera), 3'ss of exon 3
tatacttt-gttctactgggttc-ttgtcttggtttctctgaat-tgctttgccatgacttttatgcagtacacatgctaacttttattttcatgtatc--tcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGTTAAATACT
  |  ||  ||  ||  |  | | || | ||  ||||| |   | || |||    |||  || |     |||   | ||     |||||||  | || |  | |||||||||||||| || |||||||||||||||||||||||||||||||| || || || ||| ||||||||||   |||  |  | || |||||  | |||
--tgtttaagtattatagaatacattattttattttctttttgtatgttttat--tgatgttcaactcatacttgt-cttgtgattatttttgtttaccctttagCATAAACACAGTGTACTACATGGCACCTTTTGCAACCATGATCTTGGCAGTGCCAGCTATGGTACTTGAAGGTCCTGGTGTTATAGATTGGTTTCAAACT
















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|27425962|gb|CA937482.1|CA937482
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|13787854|gb|BG650446.1|BG650446
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|13791096|gb|BG653687.1|BG653687
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|16347232|gb|BI972827.1|BI972827
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|254341922|gb|GR853059.1|GR853059
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|120529232|gb|EH257366.1|EH257366
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|27425361|gb|CA936881.1|CA936881
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|9898776|gb|BE607744.1|BE607744
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|18039178|gb|BM307472.1|BM307472
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT
EST: gi|120529302|gb|EH257436.1|EH257436
EST:     GGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGNCGGT
genomic: GGATACAAATTTGACAGgtaccatctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccatgacttttatgcagtacacatgctaacttttattttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGTTAAATACT
                           tgctaac  putative branch site (score: 1)
                                       ttttcat  putative PPT
                              taacttttattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatactttgttctactgggttcttgtcttggtttctctgaattgctttgccatgacttttatgcagtacacatgctaacttttattttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGGTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGTTAAATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - tctactg
- - - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - - ctctgaa
- - - - - - - - - - - - - - - - - - - - - - ctttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct