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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatttcaaggttaatttactgttcactgttcacgtttcttcctaatcggatattcaatggtctatgcaagaaataacatatattatcccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGAATGAGGTGAAGCCTGTACCAAGGGTTGACAGTTCCGGACAGGTGTGTGG

Basic information

species Glycine max
transcript GLYMA10G38840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38840.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G22850.1 (Arabidopsis thaliana), 3'ss of exon 3
tttcatttcaag--gttaatttactgttcactgt-tcacgtttcttcctaatcggatattcaatggtctatgcaagaaataacatatat-tatcccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGAATGAGGTGAAGCCTGTACCAAGGGTTGACAGTTCCGGACAGGTGTGTGG
 |   |  ||||  |||  |    | || |     || |  |  |   | |||   |   |||   |  ||  | ||  |    | | | ||| |    | |||||| ||||||| |  |||| ||||||||||| || | ||||||||||   |||||| | ||||| ||||||||||| |||||||| ||  |||| || ||
gtatgtagcaagccgtttttcgggttttgaagacatctcactgttctttgatctagtg--caaatatgaat-taggatgtggt-tgtgtgtatgcataatgcagGATGTTTCTTTACCTCATCTGGAGGTTTGAGGAGCTATGAGCATCCATCAAATGAGTTAAAGCCGGTACCAAGGGTAGACAGTTCGGGTGAGGTTTGCGG
















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|254326314|gb|GR840906.1|GR840906
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|192295822|gb|FG990874.1|FG990874
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|7283825|gb|AW596427.1|AW596427
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTGTCTGTGCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCA
EST: gi|192333019|gb|FK024668.1|FK024668
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|23726996|gb|BU761512.1|BU761512
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|213592774|gb|DB981292.1|DB981292
EST:     GAGATCGTAACTAAGAGCTGTGGGAGAA-ATTACGCAAGATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: GAGATCGTAACTAAGAGCTGTGGGA-AATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|254343155|gb|GR859317.1|GR859317
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|208114336|gb|GD908909.1|GD908909
EST:     ATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: ATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|254320535|gb|GR826984.1|GR826984
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|6667998|gb|AW279449.1|AW279449
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|254326313|gb|GR840905.1|GR840905
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAG-TTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
EST: gi|5606908|gb|AI901006.1|AI901006
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTNNTCTTTTCAACATCC
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCC
EST: gi|254320536|gb|GR826985.1|GR826985
EST:     AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAG                         GATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA
genomic: AGAGATCGTAACTAAGAGCTGTGGGAAATCTTACGCACCATTCCCCAAAGgtaataataa ... ccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcggatattcaatggtctatgcaagaaataacatatattatcccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGAATGAGGTGAAGCCTGTACCAAGGGTTGACAGTTCCGGACAGGTGTGTGG
                            aaataac  putative branch site (score: 2)
                                        ttatccc  putative PPT
                         aagaaataacatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatttcaaggttaatttactgttcactgttcacgtttcttcctaatcggatattcaatggtctatgcaagaaataacatatattatcccatgttcagGATTTTTCTTTTCAACATCCGGAGGTTTGAGCAGTTTTGAGCATCCACTGAATGAGGTGAAGCCTGTACCAAGGGTTGACAGTTCCGGACAGGTGTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - tgttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaaga