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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaccttggccaataccaaacttaatcaaaatagttatattttattttattatgtcaacaagatggttagtcattatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA

Basic information

species Glycine max
transcript GLYMA16G17680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17680.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
-----aaaaccttggccaataccaaac-ttaatcaaaatagttatattttattttattatgtcaacaagatggttagtcattatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA
     | ||  | || || |   || | ||  |||  |   ||| | |   ||||  | | ||||| | |    ||  || |   ||     ||| ||   ||||||  ||||| |||||||||||||||| | |||||||||||||||  |||| |||||||| || ||| | ||||| ||| | ||| |||| || | ||| ||
aggaaataatttagggcattgaaaaccattcttcagtaatattacaatcagttttgattt-tcaactatac---taaccaattaagctgcaatgttata--tgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA

upper sequence: GLYMA16G17680.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g16240.1 (Oryza sativa), 3'ss of exon 1
-----aaaaccttggccaataccaaac-ttaatcaaaatagttatattttattttattatgtcaacaagatggttagtcattatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA
      ||     ||| | |   || | ||  | |  |   ||| | |  | ||||  || ||||| | |    ||  || |   ||     ||| ||   | |||   ||||| |||||||||||||||| | |||||||||||||||  |||| |||||||| || ||| | ||||| ||| | ||| |||| || |  || ||
agaactaagttagggctattgaaaaccattctttagtaatattacactc-agtttagaatttcaactatac---taaccaattaagctgcaatgttata--tccagTGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAGGATAA

upper sequence: GLYMA16G17680.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G326116_T01 (Zea mays), 3'ss of exon 3
aaaaccttggccaataccaaacttaatcaaaa--tagttatattttatt-ttattatgtcaacaagatggttagtcat-tatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA
    | |||    |||   | | | |  ||||  | ||| |   | |   |||  || |  || ||  | | | | |  ||| |  |       |  || |||||||| ||    |||||||| ||||||||||| |||||||||||| |  | |||||||| ||  |  | ||||| ||| | ||| |||| || ||||||||
---tctttgtatcatagatatccttagtaaaacttggttgttcatcaacattagcatttttactaggagatgaattaaatataggctcatgaccaccat-gcagCTATATTCTGTGATGAAGACGATGTTGCAACGTATACAATCAAGTCTGTTGATGATCCTCGCGCATTGAACAAGACACTATACATAAGACCACCAGAAAA

upper sequence: GLYMA16G17680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 2
aaaaccttggccaataccaaacttaatcaaaatagttatattttattttattatgtcaacaagatggttagtcattatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA
  |         |||   ||| ||     | | |  | ||  |  ||  ||||||     |  ||   |   |||    |  || | | |      |||||  ||||  |||||||| ||||| |||||||||| ||||||||  ||||||||||||| || ||  | ||||| ||| | ||| | ||||| ||||||||
gtacttacaattaattataaaattttgtgatacaaat-taactctttgcattatgatgg-agtatatgtgtgcat----gttttacggggtattacgcagCGGTTTTCGTGGATGAATATGATATTGCAACATACACAATCAAAACAATAGATGATCCTCGTACTTTGAACAAGACAGTTTACATTAGGCCACCAGAAAA

upper sequence: GLYMA16G17680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 2
--aaaaccttg--gccaataccaaacttaatcaaaatagttatattttattttattatgtcaacaagatggttagtcattatggcatttctgtgatgatt--gcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA
  | ||  |||  |    |   | ||| |  || |   |||| ||     |  |||   ||||     |  | | | | | ||    ||  |||   | |  | |||| ||||| |||| ||||||||||||||| |||| || ||||| |||||||||||||| || || || ||||| ||| | ||| | ||||| ||||||||
taacaattttgaagttgtttttatactgagacatag-ggttaaatccgcatacatt---tcaatggagt--tcattaaatgtgcttgtttggtggatactatgtagCTGTTTTTGTGGACGAAGATGATGTTGCAGCATACACGATCAAAGCAATAGATGATCCTCGTACACTGAACAAGACAGTCTACGTTAGGCCACCAGAAAA

upper sequence: GLYMA16G17680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0033g00270.t01 (Vitis vinifera), 3'ss of exon 2
aaaaccttggccaataccaa-acttaatcaaaatagttat--attttattttattatgt-caacaagatggttagtcattatggcatttctgtgatg-attg--cagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA
              |||  | | ||||| | || | ||    ||   | || ||||| | ||| | ||| ||  ||   |    |  || |  |  | |||   ||||  ||||  |||||||||||||||||||||||||  |||||||  ||||||||||||| || ||  | ||||| ||| | ||| | || || ||||| ||
-------------gtacttacaattaattataaaattttgtgatacaacttaattatttgcaatacgattgtgtgtatatgaaccggttttacggggtattatacagCGGTTTTCGTGGATGAAGATGATGTTGCAACATACGCAATCAAAACAATAGATGATCCTCGTACATTGAACAAGACAGTTTACATCAGACCACCAGAGAA

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|151397241|gb|EV267114.1|EV267114
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|151406310|gb|EV276125.1|EV276125
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|209718226|gb|BW657845.1|BW657845
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|192315077|gb|FK010447.1|FK010447
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAG-CAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|17401324|gb|BM178106.1|BM178106
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|192296141|gb|FG989021.1|FG989021
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|10845696|gb|BF068758.1|BF068758
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|17519561|gb|BM188603.1|BM188603
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|4313921|gb|AI461040.1|AI461040
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|14259293|gb|BG882201.1|BG882201
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|209703310|gb|BW653241.1|BW653241
EST:     TTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|298166324|gb|HO009295.1|HO009295
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|37994335|gb|CF806081.1|CF806081
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCANAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATA
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATA
EST: gi|209709206|gb|BW657175.1|BW657175
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|38191444|gb|CF920650.1|CF920650
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|192314101|gb|FK011473.1|FK011473
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|13478703|gb|BG508072.1|BG508072
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGAT
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGAT
EST: gi|7693412|gb|AW761505.1|AW761505
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTTGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|16348077|gb|BI973672.1|BI973672
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|151399718|gb|EV269589.1|EV269589
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCA-GGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|9259955|gb|BE348102.1|BE348102
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|58024852|gb|CX711593.1|CX711593
EST:     TGTGCCACCAAGGGACAAGGTGCATTTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
EST: gi|8283595|gb|BE021154.1|BE021154
EST:     TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAG                         CTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG
genomic: TGTGCCACCAAGGGACAAGGTGCATCTCTTTGGAGATGGCACACTCAAAGgtacctataa ... atgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattatgtcaacaagatggttagtcattatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA
                          tcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaccttggccaataccaaacttaatcaaaatagttatattttattttattatgtcaacaagatggttagtcattatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA

- - - - - - - - ccaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttc