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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaactcgtgatcatttaacctaatttaactgttaaaaacttattatttgatacttgagtccttgatatacgttggctggattcattttgtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGCCCAATTTGCAGGCAACCAATTGAGAGGCTTTTGGAGATAAAGGTTGGGT

Basic information

species Glycine max
transcript GLYMA19G36510.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G09770.1 (Arabidopsis thaliana), 3'ss of exon 2
gcaaactcgtgatcatttaacctaatttaactgttaaaaacttattatttgatacttgagtccttgatatacgttggc--tggattcattttgtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGCCCAATTTGCAGGCAACCAATTGAGAGGCTTTTGGAGATAAAGGTTGGGT
                | |    ||  | |   || |  ||| ||||| ||||  | ||    |  ||| | |||     | | ||   ||||    |||||||||||||||| |||||||| ||||| |||||||| |||||  || ||||||| ||||||||||||||  |||| ||||||||||||||||| |||    
---------------gtaagtgaaagctgatgatttactact-attatgtgatgatggacatatatatagatgttaaaaattgtttgggtttggtggtgcagTGTATGTGTAGCGGATGTGCTAAGGTATTGAGGTTTCAGACAAATCGATGCCCCATTTGCAGGCAACCTGTTGAAAGGCTTTTGGAGATAAAAGTTCACG

upper sequence: GLYMA19G36510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G03200.1 (Arabidopsis thaliana), 3'ss of exon 2
gcaaactcgtgatcatttaacctaat-ttaactgttaaaaacttattatttgatacttgagtccttgatatacgttggctggattcattttgtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGCCCAATTTGCAGGCAACCAATTGAGAGGCTTTTGGAGATAAAGGTTGGGT
      | ||| ||||   || |||  ||| ||  || |||   |  |||  |    |      |||| ||   |||  || |||   | ||| || ||||||||||||||| || || |||||||  || ||||| |||||  ||   |||||| ||||||| |||||  |||||| |||||||||||| ||        
---gtatagtgttcatcatacttaaaattagctcatataaaaaaaaaattgaacttct-----tttgaaatggtttg--tgtatt---tctgt-ttggcagTGTATGTGTAGCGGGTGCGCAAAGGCGTTAAGGTTTCAGACAAATCTGTGCCCAGTTTGCAGACAACCTGTTGAGATGCTTTTGGAGATTAACAAGAACG

upper sequence: GLYMA19G36510.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g01940.t01 (Vitis vinifera), 3'ss of exon 2
------gcaaactcgtgatcatttaacctaatttaactgttaaaaacttattatttgatacttgagtccttgatatacgttggctggattcattttgtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGCCCAATTTGCAGGCAACCAATTGAGAGGCTTTTGGAGATAAAGGTTGGGT
      | ||| |  ||   | |   |  |   | ||  |   |||| | |||||   |  |||       || ||    ||  ||| ||  |||  |  |||||||||||||| ||||| ||||| || |||||||||||||| |||||  | ||||| |||||| | |||| | | ||||| ||| |||||||||||||  |  
atcagggaaaattaatgccaagtcttctcaccatgaccataggaaacctgttattaatttgttgg-----cgacat-taatgattgggtttctttctttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGCCCTATTTGCCGACAACTAGTCGAGAGACTTCTGGAGATAAAGGTCAGCA

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|19053880|gb|BM732547.1|BM732547
EST:     TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|193593352|gb|FK547046.1|FK547046
EST:     GCCGGGATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: GCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|209720274|gb|BW674616.1|BW674616
EST:     TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|6072168|gb|AW101555.1|AW101555
EST:     TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|16342102|gb|BI967697.1|BI967697
EST:     GAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: GAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|208291346|gb|GE094568.1|GE094568
EST:     GCCGGCATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: GCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|31306893|gb|CD392096.1|CD392096
EST:     TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATG                         TGTATGTGTAGTGGATGTGCCAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|22523525|gb|BU082336.1|BU082336
EST:     TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: TTTGCTGGTCAGAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
EST: gi|6072057|gb|AW101376.1|AW101376
EST:     GAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATG                         TGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC
genomic: GAGCCTCGAGATACAATTGTCCATCCCTGCCGGCATATGgtatttgcag ... gtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgatacttgagtccttgatatacgttggctggattcattttgtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGCCCAATTTGCAGGCAACCAATTGAGAGGCTTTTGGAGATAAAGGTTGGGT
                ccttgat  putative branch site (score: 5)
                                    attcattttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaactcgtgatcatttaacctaatttaactgttaaaaacttattatttgatacttgagtccttgatatacgttggctggattcattttgtatttgcagTGTATGTGTAGTGGATGTGCAAAGGTTTTGAGGTTCCAGACGGATAGATGCCCAATTTGCAGGCAACCAATTGAGAGGCTTTTGGAGATAAAGGTTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
-caaactc
- - - - - - - - - - - - - - - - - taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctgg