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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaaacattattcagcttcatactttaagtgcatgctttatatgtttctagtttattgaattagcattgtttgaaaattatgttttgcattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTCG

Basic information

species Glycine max
transcript GLYMA18G01590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 4
aaaaaaaacattattcagcttcatactttaagtgcatgctttatatgtttctagtttat-tgaattagcattgtttgaaaattatgttttgcattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTCG
   | ||   |  || ||| |  | | | |||   |   |     || | ||      | ||  || | | ||     || |  |||     ||  |||||||  ||   |||||||| |  ||  |  |||| || ||||| || ||  ||||||| |||||||||||||| ||||| ||||| || ||||||||||| |
tgtacaatgttcttttagccttgtgcctgaaggttaatttccccttgatactgccccttgtggttttgtaatgaa-acaactcttgtaaaatataatgcagGGCGATAGCTTGATGAGGACACTTCATGTTGCGGCATTTGCAGTATCAGGCTATGCTTCAACTGAAGGTCGGCAATGCAAACCGTTCAATCCTTTACTGG

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------------------------------aaaaaaaacattattcagcttcatactttaagtgcatgctttatatgtttctagtttattgaattagcattgtttgaaaattatgttttgcattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTCG
                                                                                     | | |  ||    |      |  |||    || |  |||  |  | ||||    |||  ||| | || |  |   ||   | |||  ||||   ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||| |||||||||| || |||||  | ||||| |||||||| || ||| |||| |
gtcaggtcattcagcctttttttaattttagtacgatacaggaaagagtggtttattcttcaagtaggcggtttgttgttatgtgatatatgtttccaaatcgtttgttttgctggcctagtttg-aaatgtctataacattatatttg-atggcctcctaacagtctttctcatt--tcagGGTAATGAATTGATGAGGATTCTAAACATAGCAGCGTTTGCTGTATCTGGCTATGCGTCCACGGAAGGCAGGCAATGCAAACCTTTCAACCCTCTACTTG

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13170.2 (Arabidopsis thaliana), 3'ss of exon 4
-------------------aaaaaaaacattattcagcttcatactttaagtgcatgctttatatgtttctagtttattgaattagcattgtttgaaaattatgttttgcattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTCG
                      | | |  ||    |      |  |||    || |  |||  |  | ||||    |||  ||| | || |  |   ||   | |||  ||||   ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||| |||||||||| || |||||  | ||||| |||||||| || ||| |||| |
gtaggcggtttgttgttatgtgatatatgtttccaaatcgtttgttttgctggcctagtttg-aaatgtctataacattatatttg-atggcctcctaacagtctttctcatt--tcagGGTAATGAATTGATGAGGATTCTAAACATAGCAGCGTTTGCTGTATCTGGCTATGCGTCCACGGAAGGCAGGCAATGCAAACCTTTCAACCCTCTACTTG

upper sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 4
aaaaaaaacattattcagcttcatactttaagtgcat-gctttata--tgtttctagtttattgaattagcattgtttgaaaattatg-ttttgcattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTCG
  |      ||  ||    |   | ||| || ||  |  | | |||  ||  |    || ||||||||  |  ||  |||| |  ||| |||| | | | |||||| ||||| |||||||||||||| || ||||| ||||||||||| ||| ||||||| ||||| |||||||| || || ||||| ||||||||| | || |
--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|207709953|gb|GD690637.1|GD690637
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAG
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... cattgtgcagGGG-AATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAG
EST: gi|207691259|gb|GD673239.1|GD673239
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... cattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
EST: gi|193478188|gb|FK445325.1|FK445325
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... cattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
EST: gi|193493751|gb|FK461397.1|FK461397
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGATTT
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... cattgtgcagGGGAATGATTT
EST: gi|208288716|gb|GE087529.1|GE087529
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... cattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
EST: gi|193559808|gb|FK510925.1|FK510925
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... cattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
EST: gi|8282551|gb|BE020112.1|BE020112
EST:     ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAG                         GGGAATGACTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC
genomic: ACCTAGAGTATTCATACCTGGTTGATAGAGCATTGGAGTGGGGAAAGCAGgtcaggtcct ... cattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttctagtttattgaattagcattgtttgaaaattatgttttgcattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTCG
                       attgtttgaaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaaaacattattcagcttcatactttaagtgcatgctttatatgtttctagtttattgaattagcattgtttgaaaattatgttttgcattgtgcagGGGAATGATTTGATGAGAATTCTAAACATTGCAGCTTTTGCTGTGTCTAGCTATGCGTCAACTGAAGGTCGACAATGTAAACCTTTTAATCCTTTACTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
aaaaaaa
- - - - - - - -cagcttc
- - - - - - - - - - - - - - - - -gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg