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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaggagtagtgctactgctgtttttttttttcgtctgtttgtatgaccctattgattttatgaaagaaacactgttcaatattggtaggttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGACCATTTTGTTTGTTCAGAATGTTCATCTGATGATGACATGAAGAAACCC

Basic information

species Glycine max
transcript GLYMA12G35680.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G22140.2 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------taaggagtagtgctactgctgttttttt-----------ttttcgtctgtttgtatgaccctattgattttatgaaagaaacactgttcaatattggtaggtt--ttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGACCATTTTGTTTGTTCAGAATGTTCATCTGATGATGACATGAAGAAACCC
                       | |  |       ||||  |||||               | |  |||||||| ||  ||     |  | || |  | |||  | || | |  |    ||  |   | ||||||||| |||||||| || || |||||||| |||||||||||||||||  | || || ||||| ||| | |||||    |||||||| ||  | || ||| | 
gtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgttttta-aacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGATCACTTTGTATGTGCTGAATGCAGTTCTGATGACGATGTCAAAAAATCG
















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|298165839|gb|HO008810.1|HO008810
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaagccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGA
EST: gi|151409769|gb|EV279577.1|EV279577
EST:     CCATATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCATGGGCATGACTATTGAAG
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaagccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAG
EST: gi|298165969|gb|HO008940.1|HO008940
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaagccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTA
EST: gi|23734790|gb|BU765640.1|BU765640
EST:     CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG                         GTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA
genomic: CCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaagccag ... ttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccctattgattttatgaaagaaacactgttcaatattggtaggttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGACCATTTTGTTTGTTCAGAATGTTCATCTGATGATGACATGAAGAAACCC
     tattgat  putative branch site (score: 3)
                                             ttttttgt  putative PPT
     tattgattttatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaggagtagtgctactgctgtttttttttttcgtctgtttgtatgaccctattgattttatgaaagaaacactgttcaatattggtaggttttttgtagGTACCATCCTGCTTGCGTGGGCATGACTATTGAAGAAGCAAAGAAATTGGACCATTTTGTTTGTTCAGAATGTTCATCTGATGATGACATGAAGAAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - ctactgc
- - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa