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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatatatatatattcagcttcacactttaagtgcatgctttgtatgtttctagtttattgaattagcattgtttgaaaattatgttttgtattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTTG

Basic information

species Glycine max
transcript GLYMA11G37650.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 4
aaatata-tatatattcagcttcacactttaagtgcatgctttgtatgtttctagtttat-tgaattagcattgtttgaaaattatgttttgtattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTTG
   || | | |   || ||| |    | | |||   |   |     || | ||      | ||  || | | ||     || |  |||    |||  |||||||  ||  ||||||||| |  ||  |  |||| || ||||| || ||  ||||||| |||||||||||||| ||||| ||||| || ||||||||||| |
-tgtacaatgttcttttagccttgtgcctgaaggttaatttccccttgatactgccccttgtggttttgtaatgaa-acaactcttgtaaaatataatgcagGGCGATAGCTTGATGAGGACACTTCATGTTGCGGCATTTGCAGTATCAGGCTATGCTTCAACTGAAGGTCGGCAATGCAAACCGTTCAATCCTTTACTGG

upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------------aaat-atatatatattcagctt-cacactttaagtgcatgctttgtatgtttctagtttattgaattagcattgtttgaaaattatgttttgtattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTTG
                                                                                |  | |||||| | | ||  |       |||    || |  |||| |  | ||||    |||  ||| | || |  |   ||   | |||   |||   ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||| |||||||||| || |||||  | ||||| |||||||| || ||| ||||||
gtcaggtcattcagcctttttttaattttagtacgatacaggaaagagtggtttattcttcaagtaggcggtttgttgttatgtgatatatgtttccaaatcgtttgttttgctggcctagtttg-aaatgtctataacattatatttg-atggcctcctaacagtctttctcatt--tcagGGTAATGAATTGATGAGGATTCTAAACATAGCAGCGTTTGCTGTATCTGGCTATGCGTCCACGGAAGGCAGGCAATGCAAACCTTTCAACCCTCTACTTG

upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13170.2 (Arabidopsis thaliana), 3'ss of exon 4
-----------------aaat-atatatatattcagctt-cacactttaagtgcatgctttgtatgtttctagtttattgaattagcattgtttgaaaattatgttttgtattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTTG
                 |  | |||||| | | ||  |       |||    || |  |||| |  | ||||    |||  ||| | || |  |   ||   | |||   |||   ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||| |||||||||| || |||||  | ||||| |||||||| || ||| ||||||
gtaggcggtttgttgttatgtgatatatgtttccaaatcgtttgttttgctggcctagtttg-aaatgtctataacattatatttg-atggcctcctaacagtctttctcatt--tcagGGTAATGAATTGATGAGGATTCTAAACATAGCAGCGTTTGCTGTATCTGGCTATGCGTCCACGGAAGGCAGGCAATGCAAACCTTTCAACCCTCTACTTG

upper sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 4
aaatatatatatattcagcttcacactttaagtgcat-gctttgta--tgtttctagtttattgaattagcattgtttgaaaattatg-ttttgtattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTTG
  |  | ||    ||    |     ||| || ||  |  | |  ||  ||  |    || ||||||||  |  ||  |||| |  ||| ||||   | | |||||| |||||||||||||||||||| || ||||| ||||||||||| ||| ||||||| ||||| |||||||| || || ||||| ||||||||| | ||||
--acttgtaatggtttccgtctgttcttgaactgttttacatcataattgggtgatattaattgaatt--ccatgactgaagagcatggttttacctggcgcagGGAAATGACTTGATGAGAATTCTGAATATTGCCGCTTTTGCTGTATCTGGCTATGCATCAACAGAAGGTCGGCAGTGCAAACCCTTTAATCCTCTCCTTG

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|15204772|gb|BI427540.1|BI427540
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... tattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
EST: gi|7588575|gb|AW704368.1|AW704368
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGACTTGATGAGAATTCTAAACATTGCAGCTNTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... tattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
EST: gi|7588624|gb|AW704416.1|AW704416
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... tattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttctagtttattgaattagcattgtttgaaaattatgttttgtattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTTG
                           tttgaaaattatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatatatatatattcagcttcacactttaagtgcatgctttgtatgtttctagtttattgaattagcattgtttgaaaattatgttttgtattgtgcagGGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - -ttcacac
- - - - - - - - - - - - - - - - -gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg