Sequence
atgc intronic sequence ATGC exonic sequence...ccttgataagatattaattaaaaaactcaaaatttatctttgtttaattgttaggattcttgttggtcttgtataaatgcatccggtctgtatgtttcagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 4
ccttgataagatattaattaaaaaactcaaaatttatctttgtttaattgttaggattcttgttggtcttgtataa-atgcatccg-gtctgtatgttt-cagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
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---atacaggctaaccacattctttcttggtacctagtgcatctaaaataagattattcttatcgctgatatgttttatatttgcatgcttcaatgtttatagGTGTATGCCTTGACCAAAGAACGGGATACATTAAGGAGAGAGCAAAATAAAAAAAGTGATGCAGCTGCTCTTTTGAAAGAAAAGGATGAAATTATCAGTC
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G168654_T01 (Zea mays), 3'ss of exon 12
ccttgataagatat-taattaaaaaactcaaaatttatctttgtttaattgttaggattcttgttggtcttg---tataaatgcatccggtctgtatgttt-cagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
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----gtcaaaatgtacaactaatttcttttatgcatgt-ttcatctatgcatcatcttatgcatagggcataacttttaccttttttgtgccttgatgtatgtagGTATATGCACTAACCAAAGAGCGTGATACACTAAGGAGAGAACAGAATAAAAAAAGTGATGCAGCTGCCCTTTTGAAAGAAAAGGATGAGATCATCAATC
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G43330.1 (Glycine max), 3'ss of exon 7
--ccttgataagatattaattaaaaaactcaaaatttatctttgtttaatt--gttaggattcttgttggtcttgtataaatgcatccggtctgtatgtttcagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
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gaagattattaggcattatgtatatgttttgaagtgtatgctacctcatttgagctacagctgttatgggattt---tatgtgtttttggtgttta-attgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGCCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 5
ccttgataagatattaattaaaaaactcaaaatttatctttgtttaattgttagg--attcttgttggtcttgtataaatgcatccggtctgtatgtttcagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
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-tgtgtctttcttttgaggatgaagatcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgttta-attgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 5
ccttgataagatattaattaaaaaactcaaaatttatctttgtttaattgttaggattcttgttggtcttgtataaatgcatccggtctgtatgttt-cagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
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--------------gtattatatcttttatcattcttctct-ttcaattctcttc-ttttcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATCMapped 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|34544079|gb|CF512311.1|CF512311EST: AGTCTTTGCGAGAGGAATACCATCAAAGAGTAGCAGCTCTTGAAAGGAAG GTATATGCCCTTACTAAGGAAAGGGATACACTACGAGGAGAACATAACAGA
genomic: AGTCTCTGCGAGAGGAATACCATCAAAGAGTAGCAGCTCTTGAAAGGAAGgtatggtttt ... tatgtttcagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgttaggattcttgttggtcttgtataaatgcatccggtctgtatgtttcagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
gtttaat putative branch site (score: 4)
ttgtataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttgataagatattaattaaaaaactcaaaatttatctttgtttaattgttaggattcttgttggtcttgtataaatgcatccggtctgtatgtttcagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - gataaga
- - - - - - - - - taaaaaa
- - - - - - - - - - - - - tcaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatccg