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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcttgaaccctattaggtcaatgattctgagtatgtcagttcctttgttatacatgatcgtattgctgattttttttttatatgtcttgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG

Basic information

species Glycine max
transcript GLYMA19G13070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g46570.1 (Oryza sativa), 3'ss of exon 3
ttttcttgaaccctattaggtcaatgattctgagtatgtcagttcctttgttatacatgatcgtattgctgattttttttttatatg-tcttgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG
                        ||  | ||    |||   || |||   ||   || ||      | | | || |      |    | || | || ||| |||||||| || || ||||| ||  |||| ||||| || ||||| || || || || |||||||| ||||||||||||||||| ||||||||||| |||
----------------------gttggctatgttcttgtttctttcttgtctagcgattatgtctaggataaattatgagaggtgcactatttcatttcagGGTTGTTTCACTATGTATGTCACCTGTCAACGATAGTTTTATGTCAGGATCACTTGATCACAGTGTCAGGATATGGGATCTTCGTGTAAATGCTTGTCAG

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G168752_T01 (Zea mays), 3'ss of exon 3
ttttcttgaaccctattaggtcaatgattctgagtatgtcagttcctttgttatacatgatcgtattgctgattttttttttatatgtcttgctttg---cagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG
               || | |  ||  ||||    |||    | | ||| || |   ||        || |||  |      | ||||   | || |   ||| || |||||  | || ||||| ||  ||||||||||||| ||||| || || || || |||||||| || |||||||||||||||||||||||||| |||
--------------gtttgttttatttttcttctgatgctgctgcatttcttgtttgtggcaagg--gcagatgctgag---agatgttccgtttcgtctcagGGTCGTTTCATTATGTATGTCACCTGTCAATGATAGCTTTATGTCAGGATCACTTGATCACAGTGTCAGAATATGGGATCTTCGGGTAAATGCTTGTCAG

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G079723_T01 (Zea mays), 3'ss of exon 3
ttttcttgaaccctattaggtcaatgattctgagtatgtcagttcctttgttatacatgatcgtattgctgattttttttttatatgtcttgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG
 ||| ||  |   | ||   |  ||| | |||  | | |   ||   | |  | ||||  |||    || |||  |    |  |   | |    |  ||| || |||||  | || ||||| ||  ||||||||||||| ||||| || || || || |||||||| || |||||||||||||| ||||||||||| |||
gtttgttttatttt-ttcttttgatgctgctgcatttcttgtttg--tggcaacacatt-tcgaggggcagatgctgaggtgttccctttcatct--cagGGTCGTTTCATTATGTATGTCGCCTGTCAATGATAGCTTTATGTCAGGATCACTTGATCACAGTGTCAGAATATGGGATCTTCGCGTAAATGCTTGTCAG

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G14530.1 (Arabidopsis thaliana), 3'ss of exon 4
ttttcttgaaccctattaggtcaatgattctgagtatgtcagttcctttgttatacatgatcgtattgctgattttttttttatatgtcttgct-ttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG
               |  | | |     ||||    ||| | ||    | |||    |      |||| ||||         | ||||  | || || ||| ||||| || || || |||||||| || |||||||||||||||||||||||||| ||||  ||||||||  | ||||||||||| |||||||| ||||||
--------------gtctgcttataacctctggaattgtgaatttggattttactagtatgtacattgatgatgg------aaaatgttcttctgtttcagGGTTGTATCACTTTGTATGTCTCCTATAAATGATAGCTTCATGTCTGGTTCTCTCGACCGAAGTGTTAGACTCTGGGATCTTCGTGTAAATGCCTGCCAG

upper sequence: GLYMA19G13070.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g00720.t01 (Vitis vinifera), 3'ss of exon 4
ttttcttgaaccctattaggtcaatgattct----gagtatgtc--agttcctttgttatacatgatcgtat--tgctgattttttttttatatgtcttgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG
       | |    ||  ||| | | |  ||    || ||| ||  |  || |||  |  ||   |   |||  ||||||||||||| | |||| | || || || || |||||||| |||||||||||||| || ||||| |||||||||||||||||||| || |||||||| ||||| ||||||||||| |||||| ||||||||
-------gcaaatgatacggttattaaagctagtagaatatttcttatatcttttagtggacccaagtttatgatgctgatttttttctaatatttgtt-ctctgtagGGTTGTTTCCCTCTGCATGTCTCCTATTAATGACAGCTTCATGTCTGGTTCTCTTGATCACAGTGTCAGGATTTGGGATCTTCGTGTAAATTCTTGCCAG

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|192321958|gb|FK012510.1|FK012510
EST:     TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAG                         AGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC
genomic: TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAGgttagatttg ... tgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC
EST: gi|58015238|gb|CX701980.1|CX701980
EST:     TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAG                         AGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC
genomic: TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAGgttagatttg ... tgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC
EST: gi|58016158|gb|CX702900.1|CX702900
EST:     TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAG                         AGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC
genomic: TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAGgttagatttg ... tgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC
EST: gi|298184550|gb|HO029763.1|HO029763
EST:     TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAG                         AGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC
genomic: TCAATGTATGATAATCGCTGCTTACGATACTTCAAAGGGCATAAACAGAGgttagatttg ... tgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttatacatgatcgtattgctgattttttttttatatgtcttgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG
                     tgctgat  putative branch site (score: 3)
                                          tcttgcttt  putative PPT
                  tattgctgattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcttgaaccctattaggtcaatgattctgagtatgtcagttcctttgttatacatgatcgtattgctgattttttttttatatgtcttgctttgcagAGTTGTTTCTCTCTGCATGTCTCCAATCAATGATAGCTTCATGTCTGGTTCTCTAGACCACAGTGTTAGGATATGGGATCTTCGGGTAAATGCTTGCCAG

- - cttgaac
- - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatc