Sequence
atgc intronic sequence ATGC exonic sequencegtacttccttatgcattttgaattcaattatatgtttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
Basic information
species | Glycine max |
transcript | GLYMA20G11300.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 7
gtacttccttatgcattttgaattcaattatatgtttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
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--------gtaagctttttcac----attgaacattcagtatcatttt-taatttagtgcttactcatgttata-----acattgcagATCTACAGCTTGATGTCAAAGGTTGTAGTGATGTTTATGCATCATTTGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAAATATCATGCAGA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 3
--gtacttccttatgcattttgaattcaattatatgtttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgt-tagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
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gtaggttttgtcctggtaccagattgtgggttcacatt-agatgtgtttcattatttattgtcaagttaatgctgtattatggccatgcagACCTTCAACTTGATGTTAAAGGTTGTCGTGATGTGTATGCATCGTTTGATAAATATGTTGAAGTTGAGCGCCTCGAAGGTGATAATAAGTATCATGCAGA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 7
---------gtacttccttatgcattttgaat-tcaattatatgt-ttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
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gtaggtgacaaggtgaaatctggaccttgtttctttattgtttttatctattcatcatgattgtagatttatcatgta-ttttcgtaactcttttctagATCTTGCACTTGATGTCAAGGGCTGTTCAGATGTTTATGCATCATTTGATAAGTATGTTGAAGTAGAGAGATTGGAAGGTGATAATAAATACCAGTCTGA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 7
gtacttccttatgcatt-ttgaattcaattatatgtttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
||| | || | ||| | | | | | || | || ||| ||| | | || | | || ||| || |||||| || |||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| || ||||| ||||| |||||||| || ||||| ||
gtaggttctgtcatttaattgtacttgcaggaaaatcatatatttatatgatatataaataatagtt-gcctatgt-catgactggcagATCTACAACTTGATGTGAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 7
gtacttccttatgcattttgaattcaattatatg-tttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
|||||| || | |||| || || | || |||||| | ||| | || | | || | | || || || || ||| |||||||| |||||||||||||||| ||||||||||||||| ||||||||||| || |||||||| | || || |||||||||||||||||||||||
gtacttattt-tatatttatggttgaaatgcctgatttagtgtctgtttttcat----tgcaaaataaattgtt-----tgtgtggcagACCTTCAGCTGGATGTCAAAGGTTGTCATGATGTTTATGCTTCTTTTGATAAGTACGTAGAAGTTGAGCGCCTAGAAGGGGATAACAAATATCATGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
ttctaat putative branch site (score: 2)
tttgttatgtaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttccttatgcattttgaattcaattatatgtttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttagATCTTCAGCTTGATGTCAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTTGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG