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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacggtcccccccccccctccattttatttttcttgtcattttttgtatatttattgaaagaagggacgagcccaaagtgaagaatgagtaataagggttaattggttgagcagtgagcagGGTATTGTAGCTGAACGATATGGAGAGAAGCACTCCGGTGAGGAAGCCACACACTTCAACTGCAGATCTGCTTACGTGGCCTGAAACACCAATTTCTCAT

Basic information

species Glycine max
transcript GLYMA06G10930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G10930.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G78150.2 (Arabidopsis thaliana), 3'ss of exon 1
---gcacggtcccccccccccctccattttatttttcttgtcattttttgtatatttattgaaagaagggacgagcccaaagtgaagaatgagtaataagggttaattggtt------gagcagtgagcagGGTATTG-----TAGCTGAACGA-TATGGAGAGAAGCACTCCGGTGAGGAAGCCACACACTTCAACTGCAGATCTGCTTACGTGGCCTGAAACACCAATTTCTCAT
     |  |||      | |  || |||  || ||        |     | | |       ||   || ||| |  |            |   |        ||   |  ||      ||   ||  ||  | || ||     |   |||  || |||||||||||| ||||||||||| ||||||||||| || || |||||||| ||||| ||| | |||   |||    |  | 
gtaatagagtcaattaacacaatcgatta-atcttaaaccaagtgggaagaagaagctgaaaagagagagactaatcttcttcttcttcttcctctctgtatttttctcattctcttcgatttgtttgcttgctagTGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCACACACATCGACCGCAGATCTACTTACTTGGTCGGAAGTTCCACCGCCGGA-
















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|298181167|gb|HO022606.1|HO022606
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGTGAGCAG                   
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGG---AACA---A-CAGgcacggtccc ... cagt
EST: gi|9204366|gb|BE330590.1|BE330590
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGTGAGCAG                   
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGG---AACA---A-CAGgcacggtccc ... cagt
EST: gi|213589447|gb|DB973183.1|DB973183
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGTGAGCAG                   
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGG---AACA---A-CAGgcacggtccc ... cagt
EST: gi|5605824|gb|AI899922.1|AI899922
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAG                         GGTATTGTAGCTGAACGATATGGAGAGAAGCACTCCGGTGAGGAAGCCACA
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGgcacggtccc ... cagtgagcagGGTATTGTAGCTGAACGATATGGAGAGAAGCACTCCGGTGAGGAAGCCACA
EST: gi|213607251|gb|DB967044.1|DB967044
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAG                         T
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGgcacggtccc ... cagtgagcag-
EST: gi|213607251|gb|DB967044.1|DB967044
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAG                         T
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGgcacggtccc ... cagtgagcag-
EST: gi|51345323|gb|CO986056.1|CO986056
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGTGAGCAG                   
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGG---AACA---A-CAGgcacggtccc ... cagt
EST: gi|192329307|gb|FK020226.1|FK020226
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGTGAGCAG                   
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGG---AACA---A-CAGgcacggtccc ... cagt
EST: gi|209722915|gb|BW669461.1|BW669461
EST:     GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGGAACAACAGTGAGCAG                   
genomic: GAGGTCATCGTCGTCATTTCTGCGCTCGAGATTAACATAAGG---AACA---A-CAGgcacggtccc ... cagt


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgagcccaaagtgaagaatgagtaataagggttaattggttgagcagtgagcagGGTATTGTAGCTGAACGATATGGAGAGAAGCACTCCGGTGAGGAAGCCACACACTTCAACTGCAGATCTGCTTACGTGGCCTGAAACACCAATTTCTCAT
                              ggttaat  putative branch site (score: 4)
                     agtaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacggtcccccccccccctccattttatttttcttgtcattttttgtatatttattgaaagaagggacgagcccaaagtgaagaatgagtaataagggttaattggttgagcagtgagcagGGTATTGTAGCTGAACGATATGGAGAGAAGCACTCCGGTGAGGAAGCCACACACTTCAACTGCAGATCTGCTTACGTGGCCTGAAACACCAATTTCTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT