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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgcattgcaaatataatatttaatgcattactatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG

Basic information

species Glycine max
transcript GLYMA06G17470.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g70140.1 (Oryza sativa), 3'ss of exon 2
-------ttatgcattgcaaatataatatttaatgcattactatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG
       ||||   |||| | | |   |||   || | |    ||||        ||  ||   |||| | |    |  |   |||    |    |  |  ||||||||| ||||| || ||||||||||  ||||| || ||| |||| ||  |||||||||| ||||||||||| || ||  ||||||| ||||| |||||  | 
ttgtgacttatcagttgcgagtttgggattacttgaactttactggcg-------cttctttactgataactacaagtcttgatttctactccaatctatgttgaagGCACCCTAACATTAGCAGCCAAAACGGAGCAATCTGCTTGGACATACTGAAGGACCAATGGAGCCCAGCCCTTACATTGAAGACGGCACTGCTTTCCCTC

upper sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------ttatgcattgcaaatataatatttaatgcattactatggc---------ataataatctgtttggttgattaatgtgtg---gatgttttttgcgtatgt-------------taaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG
                                                                         | ||| |    | ||||   | || || |||| || ||           | || || | |    ||||  || | | |     || ||||| | | |  |             |  |  ||||||||| ||||| ||||||||||||| |||||| |||||| |||| ||  |||| || |||||||||||||| || ||  |||||||||| || |||||  | 
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacc-tacatatgccagttgatacattcctctgatcatgaacagagaacaaccagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT

upper sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
lower sequence: AT5G50870.1 (Arabidopsis thaliana), 3'ss of exon 2
ttatgcattgcaaatataatatttaatgcatta-ctatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG
 | |  || |  | | ||  |||||   || || || ||  |    | | ||      | |  | | | |   ||||  |||  | || | || ||  ||||||||| ||||| || |||||||| || || || ||| ||||||||||||| ||||||||||| ||||| || ||||||||||| || ||| ||||  | 
ctcttgatagacattttaccatttatgacaatatctttgaaactgcattgtgcgctaataaggagtttatttctgttgattg-atctgatcaaaatcaaagGCATCCGAATATTAGTAGCCAAAGCGGTGCAATATGCTTGGATATCTTGAAAGACCAGTGGAGTCCAGCTCTTACTCTGAAGACAGCTCTTGTTTCAATT

upper sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
ttatgcattgcaaat-ataatatttaatgcattactatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatg--ttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG
   | | | |   || ||||    ||| |    |  || |   | |      ||  |  || |||  |  | ||  ||||||| | ||  | | | ||| |||||| |||||||||||||| ||||||||||| |||||| |||| ||  ||||||||||||||||||| ||||| ||||||||||| ||||| |||||||| 
---tccttcgtgcatgataaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA

upper sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ07315 (Selaginella moellendorffii), 3'ss of exon 2
ttatgcattgcaaatataatatttaatgcattactatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG
         |  | |   |  |  |    |     | |    || |||||  ||  ||  ||  | ||  | || | ||  |   | |||        |||||||| |||||||||||||||| |||||| |||||||| || ||  | || |||||||||||||| || ||||| || ||||| || || |||||| | 
---------gtgagtgagagctcgagaaaag----aggaacaaaaaatctagttttttttttcctttgatgctgatcttgtctccttttacttcgcccagGCATCCCAATATCAGCAGCCAAAATGGAGCCATTTGCCTAGACATTCTCAAAGACCAGTGGAGCCCGGCTCTCACCCTCAAGACGGCTCTACTTTCTCTC

upper sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ27483 (Selaginella moellendorffii), 3'ss of exon 2
ttatgcattgcaaatataatatttaatgcattactatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG
   || | ||  |  |  | |    | | |  |  |     || |  | | |||  ||  || |||    ||| || | | | | |  |   |     |||||||| ||||||||||||||||  ||||| |||||||| || ||  | || |||||||||||||| || |||||||| ||||| || || |||||| | 
--gtg-agtgagagcacgagaaaagaggaacaa--aaaatctagt--tttttttttttctttgatgct--gatcttgtctccttttactttgccc---agGCATCCCAATATCAGCAGCCAAAACGGAGCCATTTGCCTAGACATTCTCAAAGACCAGTGGAGCCCGGCTCTCACTCTCAAGACGGCTCTACTTTCTCTC

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|151403796|gb|EV273606.1|EV273606
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGTATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|7028702|gb|AW458485.1|AW458485
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|298177912|gb|HO021937.1|HO021937
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCGGTTTAAAACCAAAGTTTG                         GCACCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|298189934|gb|HO038337.1|HO038337
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCACCCTAATATCGGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|298176063|gb|HO015468.1|HO015468
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCACCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|298184084|gb|HO029297.1|HO029297
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCACCCTAATATCAGCAGCCAAAGTGGAGCTATTCGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|4437051|gb|AI522916.1|AI522916
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|298189987|gb|HO032108.1|HO032108
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCACCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|254313570|gb|GR831199.1|GR831199
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|298180493|gb|HO022046.1|HO022046
EST:     ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTG                         GCACCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
EST: gi|58022999|gb|CX709740.1|CX709740
EST:     ATGGGTACCCGTTTGAACCCCGCAAGATGCAGTTTAAAACCAAAGTTTG                         GCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA
genomic: ATGGGTACCCGTTTGAACCCCCCAAGATGCAGTTTAAAACCAAAGTTTGgtacgaaagg ... aacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctgtttggttgattaatgtgtggatgttttttgcgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG
             gattaat  putative branch site (score: 3)
           ttgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgcattgcaaatataatatttaatgcattactatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA