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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgcttcttccataaaatgttgtctcctaaaaaataaatcagtgatattagtttctggtcaattactaaatttgcattatgctctgttgtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGATATATCTGCTGGGGATGGTACTGGAGGAGAATCTGTATATGGACTTAAGT

Basic information

species Glycine max
transcript GLYMA02G15250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G15250.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g11320.1 (Oryza sativa), 3'ss of exon 1
taatgcttcttccataaaatgttgtctcctaaaaaataaatcagtgatattagtttctggtcaattactaaatttgcattatgct-ctgttgtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGATATATCTGCTGGGGATGGTACTGGAGGAGAATCTGTATATGGACTTAAGT
 ||   |      ||| ||     | | ||  |    |||    ||  |    ||    || |||  || |       |   |    ||||||  |   ||||||||||||| ||||| ||||| |||||||| ||| | ||||| || |||||| ||||||| ||||| || ||||| || ||  | |||||  | ||||
aaactttgtcctgatacaactgcatatacttcactgaaaactgttgtcacatcttcaccgt-aatctctgagaccatgtccggtaattgttgttcttgtagGGATCTTGCTTCCATCGCGTTATCAAAGGCTTTATGGTACAAGGTGGAGATATAACTGCTGGTGATGGAACAGGAGGGGAGTCAATTTATGGGTTGAAGT

upper sequence: GLYMA02G15250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0063g01030.t01 (Vitis vinifera), 3'ss of exon 1
-----taatgcttcttccataaaatgttgtctcctaaaaaataaatcagtgatattagtttct--ggtcaattactaaatttgcattatgctctgttgtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGATATATCTGCTGGGGATGGTACTGGAGGAGAATCTGTATATGGACTTAAGT
     |  ||   ||||  |    | |         |  | ||| | |    ||  |  |||     | | || ||||  ||  |||||  ||  ||      |||||||  ||| |||||||||||||||| ||| || ||||| ||||| || ||||| ||||||||| |||||||||| || |||||  | ||||| || || |
ctcatttgtgtggcttcagttttgtctacctctgggatgactaatttaagagtacaatcttccccaataagttgctaatgtttaattata-tccatt------tcagGGAGTTTGTTTTCATCGTGTTATTAGAGGGTTTATGATACAAGGTGGAGATATTTCTGCTGGGAATGGTACTGGTGGTGAATCCATCTATGGTCTGAAAT
















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|151407281|gb|EV277096.1|EV277096
EST:     CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAG                         GGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
genomic: CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAGgtcatctttt ... gtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
EST: gi|298186510|gb|HO037143.1|HO037143
EST:     CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAG                         GGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
genomic: CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAGgtcatctttt ... gtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
EST: gi|192297055|gb|FG990326.1|FG990326
EST:     CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAG                         GGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
genomic: CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAGgtcatctttt ... gtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
EST: gi|192323805|gb|FK018586.1|FK018586
EST:     CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAG                         GGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
genomic: CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAGgtcatctttt ... gtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
EST: gi|120495931|gb|EH224098.1|EH224098
EST:     CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAG                         GGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT
genomic: CTGGTGAGAAAGGCATTGGTTCAAATACTGGAGTGCCCCTTCATTTCAAGgtcatctttt ... gtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattagtttctggtcaattactaaatttgcattatgctctgttgtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGATATATCTGCTGGGGATGGTACTGGAGGAGAATCTGTATATGGACTTAAGT
                    tactaaa  putative branch site (score: 1)
               tcaattactaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgcttcttccataaaatgttgtctcctaaaaaataaatcagtgatattagtttctggtcaattactaaatttgcattatgctctgttgtattatcagGGATCTTGCTTTCATCGTGTTATTAAAGGCTTCATGATTCAAGGAGGTGATATATCTGCTGGGGATGGTACTGGAGGAGAATCTGTATATGGACTTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA