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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaccatacacattttggaagctgcatttttcatctttcttccagataggaaactgaagttaaccaaaaaaaaaatattttaattaattttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTTTATTTTATCCCACTGCTATTGGGTCTGAACCTCA

Basic information

species Glycine max
transcript GLYMA08G07960.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 6
gcaaccatacacattttggaagctgcatttttcatctttcttccagataggaaactgaagttaaccaaaaaaaaaatattttaattaattttcatgtc-agCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTTTATTTTATCCCACTGCTATTGGGTCTGAACCTCA
| ||  || | |  |   ||| ||   ||| | || |   || |   | |  |  | |  ||||           || |  |||| || | |  |||  |||||| || ||||| |||||||||||||||||||| ||||| ||||| || || |||||||| ||  | |||||||||||||||||||| |||||||||||
gtaag-atgctctatgcagaa-ctctgtttctaatgtccttttc--gttgttacttcatcttaattg--------atgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA

upper sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 6
gcaaccatacacattttggaagc-tgcatttttcatctttcttccagataggaaactgaagtt--aaccaaaaaaaaaatattttaattaattttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTTTATTTTATCCCACTGCTATTGGGTCTGAACCTCA
|   |       |   || || | || || | | |  ||     ||| |  ||| | | | ||  |           |  |||| | |  ||||| |||||||| || |||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| |||||| | || || || |||||||||||||||||||||||
ggctctggctttacaatgcaaacatgaatgtgttaatttca---cagcttagaagcaggatttttagtgtttgcttcaccatttcattgtattttaatgtcagCAATATGCTGGGATCAGTGGTTTCCAGAGGCAGCTCGAGCTATGGTTCTTCAAGGTGCAGAGATTCTTTTGTACCCTACTGCTATTGGGTCTGAACCTCA
















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|151410591|gb|EV280406.1|EV280406
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
EST: gi|298199306|gb|HO042669.1|HO042669
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTT
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTT
EST: gi|24135848|gb|BU926358.1|BU926358
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
EST: gi|298184831|gb|HO030044.1|HO030044
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGG
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGG
EST: gi|192328547|gb|FK023551.1|FK023551
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
EST: gi|298167316|gb|HO010755.1|HO010755
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTG
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTG
EST: gi|254330221|gb|GR839774.1|GR839774
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
EST: gi|298164922|gb|HO010919.1|HO010919
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGT
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGT
EST: gi|22541663|gb|BU091506.1|BU091506
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGGTGCTT
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGG-TGCTT
EST: gi|192328548|gb|FK023552.1|FK023552
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTC
EST: gi|298178170|gb|HO023905.1|HO023905
EST:     GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTG                         CTATTTGCTGGGACCAGTGGTTTCCT
genomic: GTTTTCCAGACTAAATTAGCAAAAATTGGAGTTGgtaagaactt ... ttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataggaaactgaagttaaccaaaaaaaaaatattttaattaattttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTTTATTTTATCCCACTGCTATTGGGTCTGAACCTCA
                                     aattaat  putative branch site (score: 3)
                                           ttttcat  CT-rich tract
            aagttaaccaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaccatacacattttggaagctgcatttttcatctttcttccagataggaaactgaagttaaccaaaaaaaaaatattttaattaattttcatgtcagCTATTTGCTGGGACCAGTGGTTTCCTGAGGCAGCCCGAGCAATGGTGCTTCAAGGTGCTGAGATTTTATTTTATCCCACTGCTATTGGGTCTGAACCTCA

- - -catacac
- - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - -ttcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa