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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatagtaattctaactggtaaatagccatgtcctgttttattttccattaagctttctttctttttttgcttactttggttcttcatttgctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATTGAGTGAGGGTGAATAACTTTCTGTATAAACAGATGCAACTCTTAAGAAT

Basic information

species Glycine max
transcript GLYMA14G02100.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00310.t01 (Vitis vinifera), 3'ss of exon 3
caatagtaattctaactggtaaatagccatg--tcctgttttattttccattaagctttctttctttttttgcttactttggttcttcatttgctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATTGAGTGAGGGTGAATAACTTT-CTGTATAAACAGATGCAACTCTTAAGAAT-
  ||  || || ||  |    | |   | ||  | | ||   | | || |||| || |  ||| | |  |   |||||    | | |  |   || | | |||||||| ||||||||||| ||||||||||| || ||||| || || ||  | | ||| |  || | |  |   | || ||| || ||||   |  |||| | 
gcattttatttttatttttatagtgaacttgaatgcagtaggaatatc-attatgcatattttatatggtgatttactaaaatcccttctccact-tgttagGTGGGCAATTGTATATCTGGCACAGATGAACCCACTCATTGTCCCAATCCTCAATGAAGTGGAGTGAGATGATTCTACAAAGAG-TGCA-TGCGGAAGATTG

upper sequence: GLYMA14G02100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00270.t01 (Vitis vinifera), 3'ss of exon 3
caatagtaattctaactggta-aatagccatg--tcctgttttattttccattaagctttctttctttttttgcttactttggttcttcatttgctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATTGAGTGAGGGTGAATAACTTT-CTGTATAAACAGATGCAACTCTTAAGAAT-
    | |  ||  || |  || | |   | ||  | | ||   | | || |||| || |  ||| | |  |   |||||    | | |  |   || | | |||||||| ||||||||||| ||||||||||| || ||||| || || ||  | | ||| |  || | |  |   | || ||| || ||||   |  |||| | 
-tgcattttttaaaatttttatagtgaacttgaatgcagtaggaatgtc-attatgcatattttatatggtgatttactaaaatcccttctccact-tgttagGTGGGCAATTGTATATCTGGCACAGATGAATCCACTCATTGTCCCAATCCTCAATGAAGTGGAGTGAGATGATTCTACAAAGAG-TGCA-TGCGGAAGATTG
















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|31312032|gb|CD397235.1|CD397235
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacac ... gctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
EST: gi|21677528|gb|BQ629879.1|BQ629879
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacac ... gctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
EST: gi|213589666|gb|DB982671.1|DB982671
EST:     TACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATAACTAGCACAGATGAAACCGCTCATAGTACCTATATT
genomic: TACTGCAACAACATGCTGCTGGATGATgtaagtacac ... gctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
EST: gi|213617377|gb|DB965220.1|DB965220
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacac ... gctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
EST: gi|14991731|gb|BI317404.1|BI317404
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacac ... gctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
EST: gi|23734070|gb|BU765252.1|BU765252
EST:     ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGAT                         GTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT
genomic: ATTTCACCTAACTTTGGTTCTTACTGCAACAACATGCTGCTGGATGATgtaagtacac ... gctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattaagctttctttctttttttgcttactttggttcttcatttgctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATTGAGTGAGGGTGAATAACTTTCTGTATAAACAGATGCAACTCTTAAGAAT
                       tgcttac  putative branch site (score: 2)
         tttctttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatagtaattctaactggtaaatagccatgtcctgttttattttccattaagctttctttctttttttgcttactttggttcttcatttgctatatcagGTGGGCGATTGTATATCTAGCACAGATGAAACCGCTCATAGTACCTATATTGAGTGAGGGTGAATAACTTTCTGTATAAACAGATGCAACTCTTAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - -ctaactg
- - - - - - - - - - - - - -catgtcc
- - - - - - - - - - - - - - - - - - - - - - -ccattaa