Sequence
atgc intronic sequence ATGC exonic sequencegttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgttgtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g48770.2 (Oryza sativa), 3'ss of exon 5
gttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgttgtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
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----------------------------------------gtttgcctctattctgaaaaaacggac-ttatgtaaaatgt--gcaggattgctatatcatttt----cttaatgttgt---cagGATTTGAAGAATGCAAAATCATTAGTTGAATGGATTGCATGGGCAGAGCCTCAATATAATTTTAACCCGATGATAGATGAATGGTGCAAGGAGGCACCAA
upper sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 6
gttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgttgtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgc-agGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
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-----------------------------------------------------gtttatctctaacctgcaagtatgctgtctagcacagttggagtccattac--atttttctattggtggccagGATCTGAAGAATGCAAAATCATTGATTGAATGGATAGCGTGGGCAGAGCCTCAGTATGATTTTAATCCGATGATTGATGAATGGTGCAAGGAGGCTCCAA
upper sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G20110.1 (Glycine max), 3'ss of exon 5
gttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgttgtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
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---------------------------------gtttgcttcttttatcctttgggat-gtatggatatagag-gtcc----atggaacctttcaaaaggtctttgtacctac-atttttttcagGACTTAAAAAATGCGAAGTCAATTGTTGACTGGATTGCATGGGCTGAGCCACAATATAACTTTAATCCTATGATCGATGAATGGTGCAAAGAAGCTCCTA
upper sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G24420.1 (Glycine max), 3'ss of exon 4
gttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgttgtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
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---------------------------------gtttgcttcttttatcctttgggatt-tatggatatagag-gtcc----atggagcctttcaaaaggtttttgtacctac-atatctttcagGACTTAAAAAATGCGAAGTCAATTGTCGACTGGATTGCATGGGCTGAGCCGCAATATAACTTTAATCCTATGATCGATGAATGGTGCAAAGAAGCTCCTA
upper sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 5
gttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgtt-gtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
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gtctggtcttttttcg--ttttgaagcatttgatatgaacagtaagagctattagctattgtatgactgttcacacttctttcaac-------ttgtcttctcttttcatttctta------acagGACTTAAAGAATGCAAAGTCCATTGTTGACTGGATTGCGTGGGCGGAACCACAGTACAATTTTAATCCCATGATAGATGAATGGTGCAAGGAAGCTCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
ggcttac putative branch site (score: 3)
tatcaaaaaaaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgcatgcttttggattttaagatgattgtgataggaagtaatatctgttgtcattatatggttgttgggcatcctatcaaaaaaaaaattatatggttgttgggcttactattggttgcagGACTTAAAGAATGCAAAGTCAATAGCTGACTGGATAGCATGGGCAGAACCACAATATGACTTCAACCCTATGATTGATGAATGGTGCAGAGAAGCACCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC