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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaatatgatataatatggtatccttgtttgaagcaacgatgttttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC

Basic information

species Glycine max
transcript GLYMA20G18290.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G18290.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 1
---taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaatatg-atataatatggtatccttgtttgaagcaacgatgttttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC
   |  | |   |||  || | |  |    |||    ||  ||  ||   | | | |   | |    |  ||    || |  |  |       ||||  | |||||||||||||||||| ||||||||| | |||||||||||||| |||||  | || || || || || || |||||||||||| ||||||||| |||  ||
tattttgtgttgaatgtttatggatgggtgata----taatctgaagcgcatactttttgtgtccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC

upper sequence: GLYMA20G18290.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
--taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaatatgatataatatggtatccttgtttgaagcaa-cgatgttttg-ttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC
   |      |     ||||| |   |  | | |   |   ||  |    | | ||    |   ||| |||| || |||||  |||   || || || ||| || ||  ||||||| || ||||||||||| ||||||||||| || |||||| | || || || || |||||||| ||||| ||  |||||||||||||  | 
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacat----tggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT

upper sequence: GLYMA20G18290.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ07623 (Selaginella moellendorffii), 3'ss of exon 1
taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaatat-gatataatatggtatcct-tgtttgaagcaacgatgttttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC
                                           ||      | | |  ||  | ||  || || | ||| | |   |  | |     |  || ||| |||| || || ||||||||||| |||||||||||||| |||||  | || || |||||||| || |||||||| ||| ||||||||| |||  ||
-------------------------------------------gtaagtgttcttggcattgtttgccattctctctttcacgttccattttccccatgcagCCCACTGTTCGTGACTTGGAAGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTC

upper sequence: GLYMA20G18290.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ11024 (Selaginella moellendorffii), 3'ss of exon 1
taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaat-atgatataatatggtatcct-tgtttgaagcaacgatgttttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC
                                           ||      | |||  ||  | ||  || || | ||| | |   |  | | |   |  || ||| |||| || || ||||||||||| |||||||||||||| |||||  | || || |||||||| || |||||||| ||| ||||||||| |||  ||
-------------------------------------------gtaagtgttcatggcattgtttgccattctctctttcacgttccattttctccatgcagCCCACTGTTCGTGACTTGGAAGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTC

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|298199395|gb|HO042758.1|HO042758
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|192329677|gb|FK022943.1|FK022943
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|207765488|gb|GD738659.1|GD738659
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|24136395|gb|BU926905.1|BU926905
EST:     CTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTC
genomic: CTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACAT-GGAAGAAAGTGGTGAATGGTGGAGATCCTCGTC
EST: gi|10845842|gb|BF071193.1|BF071193
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|7327188|gb|AW621050.1|AW621050
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|209702527|gb|BW667160.1|BW667160
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|298180474|gb|HO022027.1|HO022027
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|213598937|gb|DB971951.1|DB971951
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|209727621|gb|BW663781.1|BW663781
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|4396178|gb|AI495175.1|AI495175
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|208292285|gb|GE091069.1|GE091069
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|209726453|gb|BW662818.1|BW662818
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGATAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|15285733|gb|BI469624.1|BI469624
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|27424259|gb|CA935779.1|CA935779
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACTTTTAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|208119614|gb|GD915195.1|GD915195
EST:     CCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|209708643|gb|BW678820.1|BW678820
EST:     CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
EST: gi|298192011|gb|HO036093.1|HO036093
EST:     CACAACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACA                         TCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT
genomic: CACTACAACAGCACGGAAGCTCCTTCCCCTGCCTTCGATCAGGCTCAACAgtaatccctg ... tttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacaatatgatataatatggtatccttgtttgaagcaacgatgttttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC
                                            ttttgtttt  CT-rich tract
     atatgatataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaatatgatataatatggtatccttgtttgaagcaacgatgttttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
-aaggggg
- - - - - - - - - - - - aaaataa