Sequence
atgc intronic sequence ATGC exonic sequencegtacttccttatgcattttgaattcaattatatgttttgttcttccttgttatgtatttctaatttagttttgcatatgcatgttagACCTTCAGCTTGATGTTAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
Basic information
species | Glycine max |
transcript | GLYMA13G16170.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 7
gtacttccttatgcattttgaattcaattatatgttttgttcttccttgttatgtatttctaatttagttttgcatatgcatgttagACCTTCAGCTTGATGTTAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
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-----------------gtaagctttttcacattgaacattcagtatcatttttaatttagtgcttactcatgttataacattgcagATCTACAGCTTGATGTCAAAGGTTGTAGTGATGTTTATGCATCATTTGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAAATATCATGCAGA
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 3
--gtacttccttatgcattttgaattcaattatatgttttgttcttccttgttatgtatttctaatttagttttgcat-atgcatgt-tagACCTTCAGCTTGATGTTAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
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gtaggttttgtcctggtaccagattgtgggttcacatta-gatgtgtttcattatttattgtcaagttaatgctgtattatggccatgcagACCTTCAACTTGATGTTAAAGGTTGTCGTGATGTGTATGCATCGTTTGATAAATATGTTGAAGTTGAGCGCCTCGAAGGTGATAATAAGTATCATGCAGA
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 7
gtacttccttatgcatt-ttgaattcaattatatgttttgttcttccttgttatgtatttctaatttagttttgcatatgcatgttagACCTTCAGCTTGATGTTAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
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gtaggttctgtcatttaattgtacttgcaggaaaatcatatatttatatgatatataaataatagttgcctatgt-catgactggcagATCTACAACTTGATGTGAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGA
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 7
gtacttccttatgcattttgaattcaattatatgttttgttcttccttgttatgtatttctaatttagttttgcatatgcatgttagACCTTCAGCTTGATGTTAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
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gtacttattt-tatatttatggttgaaatgcctgatttagtgt---ctgtttttcattgcaaaataaatt----gtttgtgtggcagACCTTCAGCTGGATGTCAAAGGTTGTCATGATGTTTATGCTTCTTTTGATAAGTACGTAGAAGTTGAGCGCCTAGAAGGGGATAACAAATATCATGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttgttcttccttgttatgtatttctaatttagttttgcatatgcatgttagACCTTCAGCTTGATGTTAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
ttctaat putative branch site (score: 2)
ttatgtatttctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttccttatgcattttgaattcaattatatgttttgttcttccttgttatgtatttctaatttagttttgcatatgcatgttagACCTTCAGCTTGATGTTAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG