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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacatatttacctgtcacgaggaccgattagctgtgatgcattaaacccaattgttttccacattcatctcataataactgttgattgtgttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTAACCCAGGTTAGAGTGAAATTTTTGGATGAT

Basic information

species Glycine max
transcript GLYMA19G39250.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G39250.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
atacatatttacctgtcacgaggaccgattagctgtgatgcattaaacccaa--ttgttttccacattcatctcataataactgttgattgtgttt--tagcag-
  |    ||| | | | |  || ||     ||     |   ||||||   ||  | ||  |    ||| ||   || |||||     ||| | |||   |||||      |||||  |   ||||||||| ||  | || || |||||||||||||| |||||||| || || || || || ||||| |||||||| |||||||     
-aatgagtttgctt-ttat-agaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatga-attataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----

upper sequence: GLYMA19G39250.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 4
-atacatatttacctgtcacgaggaccgattagctgtgatgcattaaaccc-aattgttttccacattcatct--cataataactgttgattgtgtttta-gcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTAACCCAGGTTAGAGTGAAATTTTTGGATGAT
 |||||||||        |         | |||     |   |  |      ||||| |  ||  || |||||   ||||    | ||| |||| |     |||  ||||| |||  ||||||||| ||  | || || |||||||||||||| ||||| || ||||| || || |||||||| || ||||| |||||||     
tatacatattctttaaatagtctatgtaactagaaagaaaatacaatcttttaattgatgcccttatgcatctattataaatgattttgtttgtttgcagTGCAAAATGGAATCTGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGCTCAAGAGGTCAGGTGACCCAGGTGAGGGTGAAGTTTTTGG-----
















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|207730894|gb|GD705135.1|GD705135
EST:     AAGCATCCCAAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: AAGCATCCC-AAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|7686526|gb|AW757174.1|AW757174
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|13481445|gb|BG510788.1|BG510788
EST:     CCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|193600669|gb|FK550766.1|FK550766
EST:     TCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: TCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|151408194|gb|EV278002.1|EV278002
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|14991990|gb|BI317663.1|BI317663
EST:     CAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|38192646|gb|CF921852.1|CF921852
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|193516142|gb|FK473824.1|FK473824
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|58018372|gb|CX705114.1|CX705114
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|193718181|gb|FK652989.1|FK652989
EST:     AAGCATCCCAAAACCCTAGCTCGCGTTCTGACTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: AAGCATCCCAAAACCCTAGCTCGCGTTCTG-CTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|192324641|gb|FK018737.1|FK018737
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|8282924|gb|BE020485.1|BE020485
EST:     CGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|208211542|gb|GE009565.1|GE009565
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|192315859|gb|FK008569.1|FK008569
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|6070105|gb|AW099677.1|AW099677
EST:     CCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|14009188|gb|BG725783.1|BG725783
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|254348341|gb|GR852020.1|GR852020
EST:     GCATCCC-AAA-CCTAGCTCGCGTTCTGCTTTCGTC-TTTACATCAGCAG                       
genomic: GCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACAT---CAGgtgcgaaaat ... gttttagc
EST: gi|8669510|gb|BE190617.1|BE190617
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGCAG                       
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACAT---CAGgtgcgaaaat ... gttttagc
EST: gi|22927955|gb|BU545094.1|BU545094
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|6915266|gb|AW396796.1|AW396796
EST:     CATGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|192297048|gb|FG991999.1|FG991999
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTCCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|151405979|gb|EV275794.1|EV275794
EST:     CAAGCATCCCGAAA-CCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|213595712|gb|DB964367.1|DB964367
EST:     CAAGCATCCCAAAACCCTAGCTTGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
EST: gi|254348340|gb|GR852019.1|GR852019
EST:     CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGCAG                       
genomic: CAAGCATCCCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACAT---CAGgtgcgaaaat ... gttttagc
EST: gi|22932959|gb|BU550098.1|BU550098
EST:     CCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAG                         GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC
genomic: CCAAAACCCTAGCTCGCGTTCTGCTTTCGTCTTTTACATCAGgtgcgaaaat ... gttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacccaattgttttccacattcatctcataataactgttgattgtgttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTAACCCAGGTTAGAGTGAAATTTTTGGATGAT
     aattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacatatttacctgtcacgaggaccgattagctgtgatgcattaaacccaattgttttccacattcatctcataataactgttgattgtgttttagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTAACCCAGGTTAGAGTGAAATTTTTGGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - ctgtcac
- - - - - - - - - - - - - - - -gctgtga
- - - - - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - - - -aacccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttg