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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgcatcttggtagtggcaagctagattcgaattttgtctattctaaatgtttgtggaaacttaaaaatttgtatgcttatattcttttgttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCATTGAAGAATGCATTAGAGCTGGGTGTTATGCAGCCAATGTTATCATCCA

Basic information

species Glycine max
transcript GLYMA13G20780.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------attgcatcttggtagt---ggcaagctagattcgaattttgtctattctaaatgtttgt--ggaaacttaaaaatttgtatgcttatattcttttgttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCATTGAAGAATGCATTAGAGCTGGGTGTTATGCAGCCAATGTTATCATCCA
                                                         |||   ||| | |      ||    | || |    ||  | ||  | | ||   |||  | |||| |||    || | |  || ||  |  ||||| ||||||| ||||| |||||||| || ||||| || ||||||||| || | |||  |||||| |||||  | |||||||  |||||||| || || |||||||||||
gtagtcggtttagaaaattatgatgtagaaacatctatgtgtcttgctttcactggatgctctttgctggcttaaacattgcatatacatccttgctttaaacgacataactgtcagtaaacataagtggttttttttttctaaacaattgtt-ttgcagGCGATGCCTTTGTTGGGGGTTTTCTCTCTCAATTGGTTCAGGAGAAGAGCATTGATGAATGTGTCAGAGCTGCTTGTTATGCTGCAAACGTTATCATCCA
















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|6071740|gb|AW101127.1|AW101127
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|10845490|gb|BF071116.1|BF071116
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACATATGGAGCAG                         GAGATGCTGTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|17518725|gb|BM187767.1|BM187767
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|6502176|gb|AW203549.1|AW203549
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|193421405|gb|FK388710.1|FK388710
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|9440259|gb|BE440768.1|BE440768
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|209697661|gb|BW655508.1|BW655508
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|9902652|gb|BE611559.1|BE611559
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAAATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|151405163|gb|EV274977.1|EV274977
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         -AGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|10232664|gb|BE801552.1|BE801552
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATNTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|21602656|gb|BQ612987.1|BQ612987
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|15287897|gb|BI471788.1|BI471788
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|308098710|gb|HO760451.1|HO760451
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|15199748|gb|BI423990.1|BI423990
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCA
EST: gi|208293408|gb|GE095104.1|GE095104
EST:     CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAG                         GAGATGCTTTTGTTGGAGGATTTACTTTCACAATTGGT
genomic: CCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagcc ... gttcttgcagGAGATGCTTTTGTTGGAGGATTT-CTTTCACAATTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatgtttgtggaaacttaaaaatttgtatgcttatattcttttgttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCATTGAAGAATGCATTAGAGCTGGGTGTTATGCAGCCAATGTTATCATCCA
 ttctaaa  putative branch site (score: 2)
                                    tattcttttgttctt  putative PPT
                 ttaaaaatttgtatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgcatcttggtagtggcaagctagattcgaattttgtctattctaaatgtttgtggaaacttaaaaatttgtatgcttatattcttttgttcttgcagGAGATGCTTTTGTTGGAGGATTTCTTTCACAATTGGTTAAGCATAAGCCCATTGAAGAATGCATTAGAGCTGGGTGTTATGCAGCCAATGTTATCATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- tgcatct
- - - - - ggtagtg
- - - - - - - - -gcaagct
- - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct