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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgaaatctagagttttgttttattttattttttggtcggggataaaagttaaaattgttgcaattggtatcttattcatacatttgatatttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCCAGCGATGAAGAGAAGAAATCCGTGTTTACCCGATTGGAAGAGGAAGTTG

Basic information

species Glycine max
transcript GLYMA10G01820.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G47470.2 (Arabidopsis thaliana), 3'ss of exon 8
gttagtgaaatctagagttttgttttattttattttttggtcggggataaaagttaaaattgttgcaattggtatcttattcatacatttgatatttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCCAGCGATGAAGAGAAGAAATCCGTGTTTACCCGATTGGAAGAGGAAGTTG
                     ||   |   | | || ||  | |    |  | ||   | |     |||||  | |||||    |   |       |||  ||||||||||||||| |||||||| ||||  |||||||| ||||| || || || || || || ||||||||  | |||||  | ||  | ||||||||||   
---------------------gtaaaaacatgtcttctg--cagaatcaccatttcccacta--aaaattgaaaacttatgttgattctatcacactctcaatagGCTGGTATAGTCGAAAGCTTAGATGCTTTGGTAAAAGAGTTAGTTGCAGCTAGTGAAGATGAGAAGAAGGCAGTGTTGTCTCGCATAGAAGAGGAAGCAA

upper sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 8
gttagtgaaatctagagttttgttttattttattttttggtcggggataaaagttaaaattgttgcaattggtatcttattcatacatttgatatttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCCAGCGATGAAGAGAAGAAATCCGTGTTTACCCGATTGGAAGAGGAAGTTG
                |||  ||   |   | | || ||  | |    |  | ||   | |     |||||  | |||||    |   |       |||  ||||||||||||||| |||||||| ||||  |||||||| ||||| || || || || || || ||||||||  | |||||  | ||  | ||||||||||   
----------------gttcggtaaaaacatgtcttctg--cagaatcaccatttcccacta--aaaattgaaaacttatgttgattctatcacactctcaatagGCTGGTATAGTCGAAAGCTTAGATGCTTTGGTAAAAGAGTTAGTTGCAGCTAGTGAAGATGAGAAGAAGGCAGTGTTGTCTCGCATAGAAGAGGAAGCAA

upper sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G47470.4 (Arabidopsis thaliana), 3'ss of exon 8
gttagtgaaatctagagttttgttttattttattttttggtcggggataaaagttaaaattgttgcaattggtatcttattcatacatttgatatttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCCAGCGATGAAGAGAAGAAATCCGTGTTTACCCGATTGGAAGAGGAAGTTG
                |||  ||   |   | | || ||  | |    |  | ||   | |     |||||  | |||||    |   |       |||  ||||||||||||||| |||||||| ||||  |||||||| ||||| || || || || || || ||||||||  | |||||  | ||                 
----------------gttcggtaaaaacatgtcttctg--cagaatcaccatttcccacta--aaaattgaaaacttatgttgattctatcacactctcaatagGCTGGTATAGTCGAAAGCTTAGATGCTTTGGTAAAAGAGTTAGTTGCAGCTAGTGAAGATGAGAAGAAGGCAGTGTTGTCTCGC----------------

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|192317314|gb|FK010545.1|FK010545
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|208102936|gb|GD900926.1|GD900926
EST:     TGAAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: TG-AGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193616592|gb|FK567790.1|FK567790
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193510278|gb|FK470262.1|FK470262
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193544830|gb|FK502147.1|FK502147
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193542813|gb|FK504134.1|FK504134
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|208304602|gb|GE106615.1|GE106615
EST:     GAGATGGAAAAGGACAACTTACTTCCCAA                         GCCGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: GAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|208159636|gb|GD953004.1|GD953004
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193714799|gb|FK651562.1|FK651562
EST:     AGGACAACTTACTTCCCTAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAG-TTGTAGCTGC
genomic: AGGACAACTTACTTCCC-AAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGC
EST: gi|6566734|gb|AW234366.1|AW234366
EST:     AGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: AGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|21993939|gb|BQ785467.1|BQ785467
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193350271|gb|FK318269.1|FK318269
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|208042619|gb|GD838665.1|GD838665
EST:     CAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: CAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|38191688|gb|CF920894.1|CF920894
EST:     GGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: GGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|10253234|gb|BE821000.1|BE821000
EST:     GGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: GGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|21639121|gb|BM140167.1|BM140167
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193538778|gb|FK496348.1|FK496348
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|192327115|gb|FK015507.1|FK015507
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|208102970|gb|GD901408.1|GD901408
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTT
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTT
EST: gi|57574002|gb|CX546977.1|CX546977
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|193467790|gb|FK433127.1|FK433127
EST:     CAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: CAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|9440203|gb|BE440712.1|BE440712
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTG
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTG
EST: gi|208210527|gb|GE015662.1|GE015662
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|207691826|gb|GD674367.1|GD674367
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|209711954|gb|BW679033.1|BW679033
EST:     AGCAAGTCGAGATGGAAAAGGACAACTTACTCCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: AGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
EST: gi|298193172|gb|HO033606.1|HO033606
EST:     ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAA                         GCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC
genomic: ATGAGAAATCTGGAGCAAGTCGAGATGGAAAAGGACAACTTACTTCCCAAgttagtgaaa ... ttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttaaaattgttgcaattggtatcttattcatacatttgatatttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCCAGCGATGAAGAGAAGAAATCCGTGTTTACCCGATTGGAAGAGGAAGTTG
                                    atttgat  putative branch site (score: 5)
                                          tatttct  CT-rich tract
                          ttattcatacatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgaaatctagagttttgttttattttattttttggtcggggataaaagttaaaattgttgcaattggtatcttattcatacatttgatatttctgtatagGCTGGTATAGTAGAAAGCTTGGATGTCTTGGTAAAGGAGTTTGTAGCTGCCAGCGATGAAGAGAAGAAATCCGTGTTTACCCGATTGGAAGAGGAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA