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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG

Basic information

species Glycine max
transcript GLYMA04G37030.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 2
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaa-attaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                                            |  | || ||| | ||     |     |||   |||  || |||||   | |  || |   | | | || | |||| |  ||  | |  |   |  || |||| |||||  |||||| ||||||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||| || |||||||| |||||  | ||
----------------------------------------------------------aaaatgcttgttgctgtttcagaagaccttgctttattgcaaggatgg---tcacttaatcttact-tattgggtcttaatatcacatttcttcttacctgcagCTTCGCAAACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGG

upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 2
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaatt-ctgactgttggctgtctc-cagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                                           | | ||| | | |  ||  |  ||| |   |  ||     | ||  ||   ||    ||| ||  ||||| || |    |  |||    ||   | | || |||| || ||  | |||| ||||||||| ||||| ||||| || ||||| |||||||||||||| ||||||||||||||||| |||||||| ||||| || ||
-----------------------------------------------------------ctgggttctct-tagttaagaaaatcgggactgat---gttcatttgtgacatgagattgtatactgtttcatatgatctcactgttctttttatatttcgcagCCTCACAAACCGTGAGGAAAATTATTGAAATAAATCCTTACATGCTGGGGACAATGGCTGGAGGTGCTGCTGATTGCCAATTTTGGCATAGGAACCTAGG

upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaat----taaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                                              | ||| |  | |||||  |  | ||     ||    || | | |  |     |   ||||    |||| ||| |  ||  || |   ||||   |   | |||||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| || || |||||||| ||||| ||
-------------------------------------------------------------aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaattt---ctgtgattgctgatgttttgtttgtgttt-ttccattcagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG

upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggca------gagttttttgtttttgtgctaattgctgcaaatta--aaatgatgggttttatctat--ttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
       |    |  |  |||| ||   || |   || | || |||  ||  ||||  |         | ||| | |||||  | ||  | ||    ||||   ||    | |     |   |   |||  |  | |||| |  ||  ||    |||||  |    | |||| || || ||||||||||| ||||| ||||||||||| |||||||| || ||||||||||| || |||||||||||||| || |||||||| ||||| ||
------gtacaatgaagattaagttagcttgttgttggttttggtt--ttgtgctggagtgtcaaacaaatttctagttttcattctgttggccattaattgtgaaccagtagaggaaagaaaacgttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG

upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G13060.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                                              ||||||   | | |  || | |   ||  ||  |  | || |      | |   |||  |  | |||| |  ||  ||    |||||  |    | |||| || || ||||||||||| ||||| ||||||||||| |||||||| || ||||||||||| || |||||||||||||| || |||||||| ||||| ||
----------------------------------------------------------ttctagttttcattctgttggccattaattgtgaaccagta-gaggaaagaaaac--gttgtgtgatttttgttaatgttttaaatctgtttaccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGG

upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                             || | ||    |  |   |     ||   | | |  |  |  || |  ||  |   || |    ||| | ||| |||||| ||   || | | || ||               |||| || || ||||||||||||||||| ||||| ||||| || |||||||| ||||||||||| || |||||||||||||||||||||||||| ||| | ||
--------------------------------------------ctcatctgatcaaaactttgaaccatgaaatagggagatcttttggactttggatgcattg--cctatttgttttcattgtcttccttccttatttttg---------------cagCATCACAATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGG

upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgc---tgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                                          |    ||||       |||  ||| ||     |    |  |  | ||  || ||||  |  |  |||  || |        | | |  | ||||         |||| ||||| || |||||||||||| | |||||||| || ||  || | || ||||||||||| |||||||| ||||| |||||||||||  | ||||| ||
---------------------------------------------------------agtgaggtttcccaaggttgcactatttaaatgtatggagcatgaagaaagggtttagttggt-acatcttgctga----caagtgc--attgtttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGG

upper sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25863 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctc-cagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                                                                                             ||  | ||| | | ||||||| |||  | || |||  |   | | |||| |||| || ||||| |||||||||||| | ||||||||||| ||| | || || || |||||||| ||||| || ||||| ||||| ||||| || ||||||||
------------------------------------------------------------------------------------------------------------gtaagtgttt-cttcgtgtttg-tctctacttgtgatcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGG

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|254321270|gb|GR824587.1|GR824587
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|58021915|gb|CX708656.1|CX708656
EST:     TATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTG-AGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: TATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|6227844|gb|AW156443.1|AW156443
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|192322800|gb|FK014491.1|FK014491
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|254322198|gb|GR837612.1|GR837612
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|8827593|gb|BE211323.1|BE211323
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|192319717|gb|FK013759.1|FK013759
EST:     GTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|151410487|gb|EV280302.1|EV280302
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|193340871|gb|FK307148.1|FK307148
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTAGAAAGAAAATTAATCGAAATCAATCC
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGT-GAA-GAAAATTA-TCGAAATCAATCC
EST: gi|15814359|gb|BI786634.1|BI786634
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|192319718|gb|FK013760.1|FK013760
EST:     GTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|298189385|gb|HO037788.1|HO037788
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
EST: gi|58014664|gb|CX701406.1|CX701406
EST:     GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATAT                         CGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA
genomic: GGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtattt ... ctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
                                ttctgac  putative branch site (score: 2)
                                             ctgtctcc  putative PPT
     tctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT