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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctggatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG

Basic information

species Glycine max
transcript GLYMA12G06990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctgg---atgccttgtttaaccaacatttctttcat--tcttgaccata--gTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG-------------
       |      ||  | |     || |   |       ||||| || |   | ||    |||   || |  |     |||| ||  ||  | ||||  |||  ||| || ||||| || ||| | || ||||||||||||||||||||||| || || || |||| ||||||| |||| ||||| |||||              
-------acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctggatgccttgtttaa--ccaacatttctttcattcttgacc-atagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG
| |  |   || || | | |||   | |   |||   |  |     ||   | ||||  ||    |||||||    |    || |||  || |        |||| || ||||| ||||||||  | ||||||||||||||||||||||||||||| || ||||   |||||||||| ||||| ||||||
tctgcatctgg-ttgtctatgatttagttt-gtatagta-aagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctggatgccttgtttaaccaaca-tttctttcattcttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG
|  || ||     ||  |   ||   |||   |   ||  || |      || || |   |  ||  ||    ||  | || |||||| ||||||    |||| || |||||||| ||| | || ||||||||||||||||||||||| ||  | || || |   |||||||||||||||| ||||||
tccaatcatcacattcatgccaacacatcat-tgcactagatcattacttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG

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|298196598|gb|HO041341.1|HO041341
EST:     CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAG                         TCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAGgtgtactgtc ... ttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
EST: gi|12774402|gb|BG239329.1|BG239329
EST:     CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAG                         TCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAGgtgtactgtc ... ttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
EST: gi|213593306|gb|DB973555.1|DB973555
EST:     CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAG                         TCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAGgtgtactgtc ... ttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
EST: gi|16277140|gb|BI942224.1|BI942224
EST:     CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAG                         TCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTTTCAGgtgtactgtc ... ttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataactttttctggatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG
                                           tcttgac  putative branch site (score: 3)
                               catttctttcattctt  CT-rich tract
                   ttgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctggatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgcc