Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA

Basic information

species Glycine max
transcript GLYMA19G38450.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027378_T02 (Zea mays), 3'ss of exon 1
-aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagta--tgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA
  |  |   ||    | |  ||||| | |  ||||    | | |  | | |||    ||  || ||  ||  || |||    | ||| ||      |||||||||||  | ||||||||  |  | |||||||| |||   ||||| || || || || ||||| ||||| || |||||||||||||||| ||||||||| ||
gtagttcctgtttttgtaacatataag-attcatttagtagagtactagtagaattcattgcattacctgcttgcgtaact-gacaaatgt-taaaaatgcagTTCCTCGAAACTTCAGGCTATTAGAGGAGCTCGAGCGTGGAGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATCTA

upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G36060.3 (Arabidopsis thaliana), 3'ss of exon 1
aaaatatggtggaaggattatatatgtagccattct-tgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA
 | || || |   | | | |    | |    |   | |     |||||   | ||   |       | |   |  ||       ||     |    |  |||||| ||||| ||| | |||||||||||||||||    ||||| ||||| || |||||||| || || || ||||||||||||||||| |||||||||||
tagat-tgttttcaagctcagtgctttgcttagaatatagagcttatttgtgttagtttccttcactaaaaattgagctgtttgatgttgttaatgtaaagTTCCGAGGAATTTCCGGTTGCTGGAGGAGCTTGAACGTGGAGAGAAAGGTATTGGAGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATTTA

upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 1
--aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA
  ||     | |||||    |   ||| | | |     ||| | | ||   ||||  || || |  | |  |||||  |   |   ||    | |  |||||| ||  | |||||||||||||||||||| |||||    || || || || || |||||||| || || |||||||||||||||||||| |||||||| ||
acaactggagttggaaatgcttggtatcttgtctcaagtgaaact-atcttagatggaa-gttacaaggtatgtgtgtttttgtctttatgttatcttgcagTCCCTCGCAACTTCAGATTGCTGGAGGAACTTGAACGTGGGGAGAAGGGTATTGGAGATGGTACTGTGAGTTATGGAATGGATGATGGAGATGACATATA

upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 2
-aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaat-gcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA
 || |  |  | ||| | | | ||  ||||| | || |    |    |     |       ||||     ||| |          ||    |  ||| | |||||| ||||||||  |  | || || || ||||||| |||||| ||||| || || |||||||| || || ||||| ||||| |||||||||||| | | 
gaagagttcatagaatgttgacat--gtagctagtcgtatgctgaggtttgattctcgctccagttctgatgtattaacttttgtttatgttcaaatcgtagTTCCTAGGAACTTTCGCCTTCTCGAAGAACTTGAGAGGGGAGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATT

upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
----aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA
       | ||| || ||   | || | |||    ||   ||||  ||| |  |  | |  | |     |   | |  | || || || |  |    | |  |||||| ||||||||  |  | || ||||||||||||| ||| || ||||| || || ||||||||||| || ||||| |||||||| || || ||  | | 
ttttttcaaatgctg-aaacttaatttttgtttttatatctgatccttagt--accttcttttttttcttttcttttaaatatgg-aactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT

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|10232200|gb|BE801079.1|BE801079
EST:     ATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: ATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|207709675|gb|GD691647.1|GD691647
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTGGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|120532072|gb|EH260205.1|EH260205
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|298194351|gb|HO040999.1|HO040999
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|298191697|gb|HO035779.1|HO035779
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|7684987|gb|AW755635.1|AW755635
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|23726374|gb|BU761179.1|BU761179
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|7042450|gb|AW472344.1|AW472344
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|9819465|gb|BE554978.1|BE554978
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|298175656|gb|HO015175.1|HO015175
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|298179361|gb|HO027832.1|HO027832
EST:     CAACACTTCTTCATCAATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|6071041|gb|AW100428.1|AW100428
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|12774302|gb|BG239229.1|BG239229
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|8826260|gb|BE209990.1|BE209990
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|13478519|gb|BG507961.1|BG507961
EST:     CAACACTTCTTCATCCACGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|23063958|gb|BU578731.1|BU578731
EST:     ATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: ATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|10231884|gb|BE800772.1|BE800772
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|13481901|gb|BG511244.1|BG511244
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|298170303|gb|HO018927.1|HO018927
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|9900251|gb|BE609219.1|BE609219
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|27427102|gb|CA938622.1|CA938622
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|298172821|gb|HO019805.1|HO019805
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|16348942|gb|BI974537.1|BI974537
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|8826180|gb|BE209840.1|BE209840
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|13311453|gb|BG405104.1|BG405104
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
EST: gi|207686937|gb|GD670465.1|GD670465
EST:     CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGG                         TTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA
genomic: CAACACTTCTTCATCCATGACGCTTGGTTCTTCAGGATCCAGTGTCGTGGgttagtatct ... tttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA
                                            ctttaat  putative branch site (score: 4)
                                           actttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - tggtgga
- - - - - - - - - - - tatgtag
- - - - - - - - - - - - - - -ccattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgcac