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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttggagactgagtaatgggcagtattaaatgcatttatattggttcacaaattgcaccgaaaagtaagaagcctgaaatttgtgttttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTGCAGCAGGACCCTCCTGTTTCCTGCAGTGCTG

Basic information

species Glycine max
transcript GLYMA10G18310.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0015g01190.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------tgttttggagactgagtaatgggcagtattaaatgcatttatattggttcacaaattgcaccgaaaagtaagaagcctgaaatttgtgttttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTGCAGCAGGACCCTCCTGTTTCCTGCAGTGCTG
                                   | || ||||||  | |   | |  | | |||          | ||  || |    |    | | |  | | ||| |||  || | || ||  ||| || ||| || |     ||||||||||| || ||||  |||||||||||||| |||||| ||||||||||   |||           
attttgcattgtctttctatggaacttgtttgatatcttatggagaa-gtgatttagttattcttactcttgacattttttatttatgcgtattgctgca--gCACGAATCCTTCAACT-GTATTG-AAACTTTGGT-CAATCTGTAATGGCTTCAAAGCGAATTAACAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACTTC-----------
















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|9819671|gb|BE555184.1|BE555184
EST:     ATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: ATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|15001120|gb|BI321934.1|BI321934
EST:     CGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: CGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|151405165|gb|EV274979.1|EV274979
EST:     AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACGCTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|19269376|gb|BM885632.1|BM885632
EST:     AAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|192333375|gb|FK024352.1|FK024352
EST:     AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|5760252|gb|AI965615.1|AI965615
EST:     GATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: GATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|8403230|gb|BE058864.1|BE058864
EST:     GCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: GCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|37995518|gb|CF807107.1|CF807107
EST:     ACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: ACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|33387783|gb|CA850990.1|CA850990
EST:     AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|298198640|gb|HO040179.1|HO040179
EST:     AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAGGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|120493582|gb|EH221749.1|EH221749
EST:     TCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: TCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|7590752|gb|AW706424.1|AW706424
EST:     CCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: CCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|24136559|gb|BU927069.1|BU927069
EST:     GCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: GCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|209697761|gb|BW663913.1|BW663913
EST:     AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|192313043|gb|FK004661.1|FK004661
EST:     AGCGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|192333374|gb|FK024351.1|FK024351
EST:     AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|209697762|gb|BW663914.1|BW663914
EST:     TCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: TCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|19453541|gb|BM954951.1|BM954951
EST:     GCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: GCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|192313044|gb|FK004662.1|FK004662
EST:     AGCGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|192322601|gb|FK014722.1|FK014722
EST:     AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: AACGCTTTCTCATCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
EST: gi|33387822|gb|CA851029.1|CA851029
EST:     ACGCTTTCTCATNCGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAG                         GTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG
genomic: ACGCTTTCTCAT-CGCTGATCAAACTTCAAACCCTAGCTAGGATTTCAAGgtatgtcgta ... ttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcacaaattgcaccgaaaagtaagaagcctgaaatttgtgttttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTGCAGCAGGACCCTCCTGTTTCCTGCAGTGCTG
                                tgaaatttgtgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttggagactgagtaatgggcagtattaaatgcatttatattggttcacaaattgcaccgaaaagtaagaagcctgaaatttgtgttttaaatttagGTACACTTAACGATGGCTTCAAAACGCATTACTAAGGAGTTGAAGGATCTGCAGCAGGACCCTCCTGTTTCCTGCAGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
tgttttg
- - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtgt