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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgttccctggagttaagctttcatgtatttggctgattttgaagaatttgcatattttattaattgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT

Basic information

species Glycine max
transcript GLYMA20G31730.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31730.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g07440.2 (Oryza sativa), 3'ss of exon 3
----tcatgttccctggagttaagctttcatgtatttggctgattttgaagaatttgcatattttattaattgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT---
    |  |  |   || | |  |  |||    || |||| |||||  ||    | |   ||  | | |  |||  ||   || |   | |  | ||  || ||||| || ||||||||||| || ||||| ||||| || |||| |||||| |||||||||||| ||   ||||| || |  ||||  |   |||| ||||| |   
gaagttctactttttgaactacaatttt---ataattgg-tgattgagatccttatcattacatgactgtttggctcaaatgttaaatctactattatttccagGGTATATATGGTTATCCTATTGAGATCCAAGCTCTATTCTACATGGCGTTGAGATGTGCTCTGCAGATGCTTAAGCCAGATGGTG---AAGGGAAGGATTTCA

upper sequence: GLYMA20G31730.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G115451_T02 (Zea mays), 3'ss of exon 3
--tcatgttccctggagttaagctttcatgtatttggctgattttgaagaatttgcat-attttattaattgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT---
  |  ||        | || |  ||  ||| | ||  ||  ||||    | | |  || |   |    |   || | |   | |  ||||||   | || ||||| || ||||||||||| || ||||||||||| || ||||  |||||||| ||||||||| |   |||||| || |  || | ||   |||| ||||| |   
acttttgaattacata-ttgattttaaatgaagtttcctt-ttttattaattctaaatgaagcttcccaccattgcatgatcgtaatttcttcaatttt-cagGGTATATATGGTTATCCCATTGAGATTCAAGCCCTATTCTATATGGCATTAAGATGTGCTCTCCAAATGCTCAAGCCAGAGGGCG---AAGGGAAGGATTTCA

upper sequence: GLYMA20G31730.2 (Glycine max), 3'ss of exon 3
lower sequence: AT4G09510.1 (Arabidopsis thaliana), 3'ss of exon 3
tcatgttccctggagttaagctttcatgtatttggctgattttgaagaatttgcatattttatta-attgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT---
              || |    | | | |   ||   ||     || |  ||  ||  || || | | |    |     |||  ||| ||| ||  |  ||||  ||||||| |||||||||||||||||||| || || ||||||||||||||||| || ||||| ||||| ||||  || ||    |||||    || |   
--------------gtaagaactaccttttagtgaacgagc--aaaaatcttatatgattcatcacactaaaaccaaatcttgatttgtttatttat-tagGGTGTTTATGGATATCCAATAGAGATTCAAGCTCTGTTTTTCATGGCATTGAGATGCGCCTTGTCGATGCTTAAACCAGACGAG---GAAGGTCGAGATTTCA

upper sequence: GLYMA20G31730.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G35580.3 (Arabidopsis thaliana), 3'ss of exon 3
tcatgttccctggagttaagctttcatgtatttggctgattttgaagaatttgcatattttattaattgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT
          |  |   || |||| ||  |     |||||| |      ||    | |||   || |    |    | |||  |||   | |  ||| ||||  ||||||| ||||| || ||||| |||||  | ||||||||||| ||||||| ||||||||| ||| | || |  ||||  |  |   || |||   
------gtattaaaagcaatctttgatcga---aactgattgttgtttcttgttttgtttggctattaagattgatttcttttttttcctgtatttgaagGGTGTTTATGGGTATCCCATTGAGATCCAAGCGTTGTTCTTCATGGCTTTGAGATCTGCTTTGTCGATGTTAAAGCCCGATGGAGATGGCAGAGAGGTCA

upper sequence: GLYMA20G31730.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0072g01040.t01 (Vitis vinifera), 3'ss of exon 3
tcatgttccctggagttaag--ctttcatgtatttggctgattttgaagaatttgcatattttattaattgtttcttctgcttccttt--cttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT---
    ||||  |    | |||  ||||   ||  |  |    |    |  ||  || ||   | |    ||    | | || |  | |    ||| || |  ||||| ||||||||||||||||| || |||||||||||||||||||||||| |||||||||||||| ||||||| |||||    ||| | ||||| || ||||   
----gttcattattttcaagagctttgtagttgtcagaaagtacatattaacatgtatgaatcacatgttaacacgtttgatcacatggattttattttgacagGGTATTTATGGTTATCCAATTGAAATTCAAGCACTTTTCTTCATGGCACTGAGATGTGCTTTGGCAATGCTAAAACAA---GACTCTGAAGGTAAAGAATGTA

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|151401362|gb|EV271176.1|EV271176
EST:     TTCCAACTTTGCTTTGTGCTAATGGATGTTGCATGGTTGATCGAAGAATG                         GGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTG
genomic: TTCCAACTTTGCTTTGTGCTGATGGATGTTGCATGGTTGATCGAAGAATGgtaagatata ... tttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTG
EST: gi|208308593|gb|GE103721.1|GE103721
EST:     TTCCAACTTTGCTTTGTGCTGATGGATGTTGCATGGTTGATCGAAGAATG                         GGTATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTG
genomic: TTCCAACTTTGCTTTGTGCTGATGGATGTTGCATGGTTGATCGAAGAATGgtaagatata ... tttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTG
EST: gi|254327978|gb|GR834943.1|GR834943
EST:     TTCCAACTTTGCTTTGTGCTGATGGATGTTGCATGGTTGATCGAAGAATG                         GGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTG
genomic: TTCCAACTTTGCTTTGTGCTGATGGATGTTGCATGGTTGATCGAAGAATGgtaagatata ... tttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatttgcatattttattaattgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT
               tattaat  putative branch site (score: 2)
            ttttattaattgtttc  CT-rich tract
         atattttattaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgttccctggagttaagctttcatgtatttggctgattttgaagaatttgcatattttattaattgtttcttctgcttcctttcttttttcttgcagGGCATTTATGGTTATCCAATAGAGATTCAAGCACTTTTCTTCATGGCATTGAGATGTGCTTTGTCAATGCTGAAACAGGATGACGCCGAAGGAAAGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
-catgttc
- - - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - tggctga
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcatat