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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagacgtgacagtgcttttgtttccactagtgataatattaacaataatgattgtagtagtagtagcagtctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC

Basic information

species Glycine max
transcript GLYMA20G35970.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g02320.1 (Oryza sativa), 3'ss of exon 6
acagacgtgacagtgcttttg------tttccactagtgataatat------taacaataa-tgattgtagtagtagtagcagt-----ctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
| || ||| |||| | | |||| || ||| | || || || |||| ||| | | | | | ||| ||| ||||||| | ||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||| | | || ||||| || || ||||| || ||||| | || || |
---gtagtactagtcctttcagctaattcttggctagcgagtctatgttttatggcagtatctgcttgttttagcctcaatgtttacctcctaatgaaggcttttcagttgttatcagTCTTTCAAGGAAATGGTTGCAATGTGCCTGGTCAAAGATCAAACAAAGAGGCCAACGGCTGAAAAGTTACTAAAGCACTCATTTTTCAAGAACGCAAAAC

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g37480.2 (Oryza sativa), 3'ss of exon 2
-------------acagacgtgacagtgcttttgttt-ccactagtgataa-tattaacaataatgattgtagtagtagtagcagtctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
| | | | |||| || | | || || || ||| || ||| ||| | | || | ||||||||| | || | |||||| ||||| || ||||| |||||||| |||||| |||||||||||||||||||||| ||| | | ||||||||||| || || || || |||||| | || || |
gtagtatccattcatctaaatattgaccatgaagtttgtcattgttttcaactactacaaattat-attatagaatt--tacctttctaattaa-gcatatt---ttgtgatcagTCATTTAAGGAGATGGTTGCAATGTGCTTGGTAAAAGATCAAACAAAGAGACCAACAGCTGAGAAGTTGCTAAAGCATTCATTTTTCAAAAATGCAAAAC

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G073399_T01 (Zea mays), 3'ss of exon 6
---------acagacgtgacagtgcttttgtt-tccactagtgataatattaacaataat-gattgtagtagtagtagcagtctaattaa---agtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
| | | | ||| | || | | || ||| | | ||| || || | | |||| ||| ||| | |||| ||||||||||||||| || || ||||||||||| |||||| |||| ||||||||||||||||| ||| | | ||||||||||| || || || || |||||| | || ||||
gtagtacctattctttcagttgatttatcgttatgaaccatttatgcggttagctacaatagactgcattc-tagtgtttacctatctaagtaggcattttcagttgtgaccagTCATTTAAAGAAATGGTTGCAATGTGCTTGGTCAAAGATCAAACAAAGAGACCAACAGCTGAGAAGTTGCTTAAGCATTCATTTTTCAAAAATGCAAAGC

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G073399_T02 (Zea mays), 3'ss of exon 6
---------acagacgtgacagtgcttttgtt-tccactagtgataatattaacaataat-gattgtagtagtagtagcagtctaatta---aagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
| | | | ||| | || | | || ||| | | ||| || || | | |||| ||| || | | |||| ||||||||||||||| || || ||||||||||| |||||| |||| ||||||||||||||||| ||| | | ||||||||||| || || || || ||||||
gtagtacctattctttcagttgatttatcgttatgaaccatttatgcggttagctacaatagactgcattc-tagtgtttacctatctaagtaggcattttcagTTGTGACCAGTCATTTAAAGAAATGGTTGCAATGTGCTTGGTCAAAGATCAAACAAAGAGACCAACAGCTGAGAAGTTGCTTAAGCATTCATTTTTCAAA----------

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G124550_T02 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------------------acagacgtgacagtgcttttgtttccactagtgataatattaacaataatgattgtagtagtagtagcagtctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
| | || ||||| |||| ||| | ||| ||| || |||| || | | |||||| ||||| ||| ||| ||| | ||||| ||||||||||||||||| |||||| |||| ||||||||||| ||||||||| | | || || || || || || || || ||||| | || || |
gtagtactagtccttttggtaaattcttgggcagtgaattttttctgattatattttttctgtgattttgtcacaagctttctgttctagaatgctgtcacagtcattttttttatag-agtctgggccttaggttagattgttgtggttgctct-----tctaatgaaagt-ttttcagctgtaatcagTCCTTCAAGGAAATGGTTGCGATGTGCTTGGTGAAAGATCAAACGAAGAGGCCAACAGCTGAAAAATTACTTAAGCATTCTTTTTTCAAGAATGCAAAAC

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G413544_T01 (Zea mays), 3'ss of exon 6
------acagacgtgacagt--gcttttgtttcc--actagtgataatattaacaataatgattgtagtagtagtagcagtctaattaa---agtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
| | | |||| | | | | | || | | || ||| | | | | | || |||| ||| ||| | |||| ||||| ||||||||| || || || |||||||| |||||| |||| ||||||||||||||||| ||| | | ||||||||||| || || || || |||||| | || ||||
gtagtacctatcctttcagttggttatcagtgactaaccatttatgtggttagctacagtagatcgtgttctagtgtttacctatctaagggggcattttcagttttgaccagTCATTTAAAGAGATGGTTGCAATGTGCTTGGTCAAAGATCAAACAAAGAGACCAACAGCTGAGAAGTTGCTAAAGCATTCATTTTTCAAAAATGCAAAGC

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G24100.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------acagacgtgacagtgcttttgtttccacta-gtgataatattaacaataatgattgtagtag--tagtagcagtctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
|| || | | |||| | | | | | | | ||| | || | || | |||| || || | || |||||||| |||||| || || ||||||||||| ||||| |||| |||||||||||||| |||||| | | || || |||| || ||||||| |||||||| | ||||
gtactcgtgttctttctaggtgtatttcttatgctgttctagttttgctagattttctgttttttcatttgcaataaatttttactaaactaactagaggactttcagttgtgcccagTCCTTTAAAGAAATGGTTGCAATGTGTTTGGTGAAAGATCAAACAAAAAGGCCAACTGCTGAAAAACTGCTGAAGCACTCCTGTTTCAAACACACGAAGC

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02480.t01 (Vitis vinifera), 3'ss of exon 6
--acagacgtgacagtgcttttgtttccactagtgataatattaacaataatgattgtagtagtagtagcagtctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
|| | | | | | |||| || | | | || | || || | |||||||| || |||||||||||||| |||||||| || ||||||||||| |||||| |||| |||||||||||||| |||||| | | |||||||| || ||||| ||||| ||||| || |||||||
ctacctggtttaagtcagtcacaatggttcgagtg-tagttgctatgttgtgttttcttacag-agcaatgttctaattagaggatttccagttgtgatcagTCTTTTAAAGAAATGGTTGCAATGTGCTTGGTGAAAGATCAAACAAAAAGGCCAACTGCTGAGAAGTTACTAAAACATTCCTTTTTCAAGCAAGCTAAGC

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|6567234|gb|AW234845.1|AW234845
EST:     AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAG                         TCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG
genomic: AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAGgtatgggtgt ... ttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG
EST: gi|10845866|gb|BF068902.1|BF068902
EST:     AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAG                         TCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG
genomic: AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAGgtatgggtgt ... ttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgattgtagtagtagtagcagtctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC
                        gtctaat  putative branch site (score: 3)
 tctaattaaagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagacgtgacagtgcttttgtttccactagtgataatattaacaataatgattgtagtagtagtagcagtctaattaaagtatttccagttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGGCCATCCGTGGAGAAGTTGCTCAAACACTCCTTCTTCAAACAGGCTAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - cagtgct
- - - - - - - - - -tgtttcc