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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatctttatctcccttgattgctattaaactttaactttcaacaagtgtttatttattgcttttaaacattctgactgggtaattgcttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTGGTGTGGCACTCTACTCGTTCATCAAAGCCAGAATGGAGGAAGAAAAGCG

Basic information

species Glycine max
transcript GLYMA13G24360.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 10
gtaaatatctttatctcccttgattg--ctattaaactttaactttcaacaagtgtttatttattgcttttaaacattctgactgggtaattgcttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTGGTGTGGCACTCTACTCGTTCATCAAAGCCAGAATGGAGGAAGAAAAGCG
|||||| |   | | |    || |||   |  | |    |  |||    | |    | ||    |||    ||    ||| || | |||    ||||  |||||||||||||||   || ||||||||||||||||||  | ||||||||||||| |||||| | ||||| ||||| || ||||  ||||| || || || ||
gtaaatgttcatcttttttctgtttgatttgcttattgctgccttctccctaaacatcata---tgcccagaagatatctaacagcgta----cttctcacagGTAACAAGATTTCAACACAAACTGGTATTGGAACATGCGTTGCAATTGCTGGAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACG
















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|5753077|gb|AI960364.1|AI960364
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|193681309|gb|FK622023.1|FK622023
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|193417392|gb|FK383868.1|FK383868
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|9903135|gb|BE612103.1|BE612103
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|207835871|gb|GD806554.1|GD806554
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|31308505|gb|CD393708.1|CD393708
EST:     ATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAAATTGCT
genomic: ATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAA-TTGCT
EST: gi|6134862|gb|AW133255.1|AW133255
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|193305382|gb|FK271341.1|FK271341
EST:     CGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGTCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCT
genomic: CGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAG-CACCCAAACTGGTATTGGAACAGCCATTGCAATTGCT
EST: gi|208264750|gb|GE062124.1|GE062124
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|9440042|gb|BE440553.1|BE440553
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|20812531|gb|BQ297009.1|BQ297009
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|19053945|gb|BM732612.1|BM732612
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|7692256|gb|AW760367.1|AW760367
EST:     GTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|17519168|gb|BM188210.1|BM188210
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|9903168|gb|BE612136.1|BE612136
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|193341828|gb|FK308916.1|FK308916
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|5677127|gb|AI938257.1|AI938257
EST:     GAACGTACTGAAACGTGTATTTGGCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|7690957|gb|AW759092.1|AW759092
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|10845091|gb|BF068262.1|BF068262
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|15000011|gb|BI320825.1|BI320825
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|208076403|gb|GD874324.1|GD874324
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|5753079|gb|AI960366.1|AI960366
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|208202709|gb|GE001777.1|GE001777
EST:     TATTATAGTCTTCG                         GTTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCT
genomic: TATTATAGTCTTCGgtaaatatct ... cttcatacagG-TAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCT
EST: gi|23057431|gb|BU578105.1|BU578105
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|6482509|gb|AW201766.1|AW201766
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCACACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|151395328|gb|EV265199.1|EV265199
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
EST: gi|7691830|gb|AW759950.1|AW759950
EST:     GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCG                         GTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTCATTGGATTCTCTATTATAGTCTTCGgtaaatatct ... cttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagtgtttatttattgcttttaaacattctgactgggtaattgcttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTGGTGTGGCACTCTACTCGTTCATCAAAGCCAGAATGGAGGAAGAAAAGCG
                            ttctgac  putative branch site (score: 2)
                                          ttgcttc  putative PPT
       tttatttattgctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatctttatctcccttgattgctattaaactttaactttcaacaagtgtttatttattgcttttaaacattctgactgggtaattgcttcatacagGTAACAAGATTAGCACCCAAACTGGTATTGGAACAGCCATTGCAATTGCTGGTGTGGCACTCTACTCGTTCATCAAAGCCAGAATGGAGGAAGAAAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA