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-agcaatgttctaattagaggatttccagttgtgatcagTCTTTTAAAGAAATGGTTGCAATGTGCTTGGTGAAAGATCAAACAAAAAGGCCAACTGCTGAGAAGTTACTAAAACATTCCTTTTTCAAGCAAGCTAAGCMapped 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|AW234845EST: AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAG TCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG
genomic: AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAGgtatgggtgt ... ttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG
EST:
gi|10845866|gb|BF068902.1|BF068902EST: AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAG TCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG
genomic: AGAATGCTCCTCCGGGGCTTGATTATGATCGTGATAGAAAGTTCTCCAAGgtatgggtgt ... ttgtgaccagTCTTTCAAGGAAATGGTTGCTATGTGCCTGGTAAAAGATCAAACAAAGAGG
atgc intronic sequence ATGC exonic sequenceIntronic 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