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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaccaggtgtccaagtatcatatttttattaattctcaaaattaaagatatcaacacgataacttaccctgtttgtttttgtgtgcgctaattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCTCCATTTTTCCTAGCATCTGCTGTGTTGTTTGCCATCAAGGATGCCATCA

Basic information

species Glycine max
transcript GLYMA13G41520.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 13
ctcaccaggtgt-ccaagtatcatatttttattaattctcaaaattaaagatatca-acacgataacttaccctgtttgtttttgtgtgcgctaattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCTCCATTTTTCCTAGCATCTGCTGTGTTGTTTGCCATCAAGGATGCCATCA
   | ||    |   ||  |  || ||    |   |  |  ||||  || ||||   |||   | | ||  | || |  |   | | |  | ||  ||  |||||  |||||||   ||||||||||||||||| || ||||| ||||||||||||||||| || || ||  |||| || || |||||||| ||||| ||  
--gatcaatcatattaaacagaatgttgcagtagttcatttaaatctaaaatattttacattgtgatttctcttgctcatgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG
















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|193559277|gb|FK512102.1|FK512102
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATG
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATG
EST: gi|308222717|gb|HO760627.1|HO760627
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|254341946|gb|GR853083.1|GR853083
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|254337732|gb|GR845302.1|GR845302
EST:     TCCTTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TCC-TTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|19347109|gb|BM891989.1|BM891989
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|8284147|gb|BE021706.1|BE021706
EST:     TCCTTCTGTGAATGATGTTTCCTTCAAATTTAATGTCTCACTCCTGGAAG                         G-TCATCCAAATGTTA-GGCCA
genomic: TCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTG-AAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCA
EST: gi|8401863|gb|BE057497.1|BE057497
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAATGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|7146051|gb|AW507973.1|AW507973
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|13788348|gb|BG650940.1|BG650940
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|10708936|gb|BF008721.1|BF008721
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|254343201|gb|GR856905.1|GR856905
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
EST: gi|10709625|gb|BF009349.1|BF009349
EST:     TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAG                         GGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT
genomic: TTCCTTCTGTGAATGATGTTCCCTTCAAATTTAATGTCTCACTCCTGAAGgtatgttcct ... taattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagatatcaacacgataacttaccctgtttgtttttgtgtgcgctaattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCTCCATTTTTCCTAGCATCTGCTGTGTTGTTTGCCATCAAGGATGCCATCA
                            tttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcaccaggtgtccaagtatcatatttttattaattctcaaaattaaagatatcaacacgataacttaccctgtttgtttttgtgtgcgctaattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCTCCATTTTTCCTAGCATCTGCTGTGTTGTTTGCCATCAAGGATGCCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
ctcacca
- - - - - - ccaagta
- - - - - - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgcg