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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgagtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC

Basic information

species Glycine max
transcript GLYMA18G52210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 2
--agtgagtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC
  ||  ||  || ||   ||   |      |     | | || ||  |   |||  |  | |     | |   | | || | |    | | | |     ||||||||||||||| |||||||| ||  ||||||| || ||||| ||  |||||||||||||||| || ||  | ||||| |||||||||||||| ||||| 
tcagc-agagctattctcatgcggtcatgcctataatcacctccataagtgactccattatactccatatgcacatcctaacttccaggtctattttgtagGTGTTGATATCAGCATGAACACGCACCTGAAAACTGTGAAACTCACATTGAAAGGGAAAAATCCTGTTACCTTTGATCACCTCAGTGTGAGGGGAAACAA-

upper sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 3'ss of exon 2
agtgagtcctcttactatattgctgcttcctagttgaa------ctacaccaacaa---ctttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC
      || | || |||  || || | |  | |||||        ||     ||||     ||| | |  | | | ||    | |||||||    |  |||    ||||||| ||||| || |||||||| || ||||| || ||||| || ||  |||||||||||||||| || || || || || ||||||||||| || ||||| 
------tcatgtttctagctttcttcatgttggttgaggtgtttttaggtggacaaggctgttatgtcctggaatgtttcaattctgattcatcaaccttt--tgcagGTGTGGATATAAGCATGAACACCCACTTGAAGACTGTTAAGCTCACATTGAAAGGGAAAAATCCTGTAACCCTTGACCACCTCAGTGTGAGAGGAAACAA-

upper sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
--agtga-gtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtct-tagctta--ctgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC
    | |  |||  |||  ||  |    | | | | |   | |  || |  ||   ||  |     | ||  |||  ||  |||||| |  |   ||||    ||||||||| ||||| ||||| || ||| |||| || || || || || || |||||||||||||| || || || ||||| || ||||||||||| ||||| 
tttttaacatcccattaaaattctctcccattcca-tcagattttac-agtaatcctagaatgattattcagtagtgtattctgattttttggactttgt---agGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA-

upper sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
------agtgagtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC
        |  ||   |||  | |         || |  ||  | | ||   |  | |  ||  ||   | |  ||   ||   | |   |     ||    ||||||| ||| | || |||||||| ||||| ||| | || ||||| |||||||||||||| |||||||| ||  | || ||  | ||||| ||||| ||||| 
tgtttggtttggtttcctttttctgccatca--tcttgtttagaatgcaattatcaatc-aactcactgactggta--ctatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA-

upper sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 4
----agtgagtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC
    | |   |       |  | ||  ||     |  |  |  |  |    ||  | |     ||| ||  |    ||| ||  | ||   |  |||  | |||||||||||| |||||||||||||||||||| ||||| ||||| ||  |||| |||||||||||||||||||| |||||  | ||||| || || ||||| 
atcaaatagataactaggcagttttaatgggaattcatgca--tgaattctcagttgtgttgaaggcagattctaattagtggctttgcc-tgcttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGAAGGGGAAAAATCCAGTGACTCTAGATCACTTGAGTGTTAGAGGCAACAA-

upper sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 2
agtgagtcctcttactatattgctgcttcctagttgaactacaccaa--caactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC
||| | |     ||    | | |   ||   |    |||||     |  |||   | |     ||  || | ||| | || |  ||   | | ||  | |||||| ||||| |||||||||||||||||||| || || ||||| |||||||| |||||||||||||||||| ||||||| || ||||||||||| ||||| 
agtaacttgaagtaggtaagtccatgttatgacaaaaactatttagaatcaaagatgattggagagatcattgctga-tggtattgctttgtatgttatagGTGTGGATATTAGTATGAACACACATTTGAAGACTGTGAAACTGACTCTGAAGGGGAAAAATCCAGTGACTATGGATCACCTGAGTGTGAGGGGCAACAA-

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|17519318|gb|BM188360.1|BM188360
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|192328861|gb|FK023263.1|FK023263
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|31473009|gb|CD415037.1|CD415037
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|298192082|gb|HO036164.1|HO036164
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGGACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|23728045|gb|BU762064.1|BU762064
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|33388742|gb|CA851949.1|CA851949
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|298175521|gb|HO018232.1|HO018232
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTGGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|26047967|gb|CA784599.1|CA784599
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
EST: gi|298174943|gb|HO014860.1|HO014860
EST:     GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGG                         TGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA
genomic: GTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGGtttcttttct ... ttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC
                            tactgat  putative branch site (score: 2)
                                          tttttgcc  putative PPT
                                         attttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgagtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC

- - - - - - - - - -ttgctgc
- - - - - - - - - - - - - - - - - - - ctacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg