Sequence
atgc intronic sequence ATGC exonic sequence...aatctacaagtacttccaggcttttgtcgaataaatattgcattgatgcatatttggttaaatcttgtgatgttgtttgctcaattatttttttcttcagTGGTAACTGTCAATGATTATCTGGCCCAACGTGATGCTGAGTGGATGGGTCGTGTTCATCGTTTCCTAGGTCTTTCAGTGGGTCTTATTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g08980.1 (Oryza sativa), 3'ss of exon 3
--aatctacaagtacttccaggcttttgtcgaataaatattgcattgatgcatatttggttaaatc-ttgtgatgttgtttgctcaattatttttttcttcagTGGTAACTGTCAATGATTATCTGGCCCAACGTGATGCTGAGTGGATGGGTCGTGTTCATCGTTTCCTAGGTCTTTCAGTGGGTCTTATTCAG
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cgcgtatgcattgatctgtcgcacttagaacatttcatattaagctc-tatttatcttttcctttcattcagattttataagcactgtgatcctttt--tcagTTGTGACTGTAAATGATTATTTGGCACAGCGAGATGCTGAATGGATGGGTCGTGTGCATCGTTTTCTTGGTCTTTCCGTGGGTCTAATTCAG
upper sequence: Vv18s0001g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G090086_T01 (Zea mays), 3'ss of exon 4
----aatctacaagtacttccaggcttttgtcgaataaatattgcattgatgcatatttggttaaatcttgtgatgttgtttgctcaattatttttttcttcagTGGTAACTGTCAATGATTATCTGGCCCAACGTGATGCTGAGTGGATGGGTCGTGTTCATCGTTTCCTAGGTCTTTCAGTGGGTCTTATTCAG
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atgcattgcacatctagtgttaggctctgctcaagttagctctcaatgtctgtcttccctattattccttcaca-attgagcactg---caatccttttttcagTGGTGACTGTAAATGATTATTTGGCACAGCGTGATGCTGAATGGATGGGTCGTGTTCATCGCTTTCTCGGTCTTACTGTTGGTCTGATTCAG
upper sequence: Vv18s0001g01860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G12320.1 (Glycine max), 3'ss of exon 3
---------------aatctacaagtacttccag-gcttt-----tgtcgaataaatattgcattgatgcatatttggttaa-atcttgtgatgttgtttgctcaattatttttttcttcagTGGTAACTGTCAATGATTATCTGGCCCAACGTGATGCTGAGTGGATGGGTCGTGTTCATCGTTTCCTAGGTCTTTCAGTGGGTCTTATTCAG
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gtatgtgaccgtgtgttattgctaacactctaaaagctttggatatgccggagaattttttcgataccagctcttggctttatgaaaaataaacttatctgatccgtgatttcttcg--cagTGGTAACTGTCAATGATTATTTAGCTCAACGTGATGCTGAATGGATGGGACGTGTTCATCGTTTCTTAGGTCTATCTGTTGGCCTTATTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcatatttggttaaatcttgtgatgttgtttgctcaattatttttttcttcagTGGTAACTGTCAATGATTATCTGGCCCAACGTGATGCTGAGTGGATGGGTCGTGTTCATCGTTTCCTAGGTCTTTCAGTGGGTCTTATTCAG
cattgat putative branch site (score: 4)
ttatttttttcttc putative PPT
tcaattatttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatctacaagtacttccaggcttttgtcgaataaatattgcattgatgcatatttggttaaatcttgtgatgttgtttgctcaattatttttttcttcagTGGTAACTGTCAATGATTATCTGGCCCAACGTGATGCTGAGTGGATGGGTCGTGTTCATCGTTTCCTAGGTCTTTCAGTGGGTCTTATTCAG
- - - - - -acttcca
- - - - - - - - - - - - - - gaataaa
- - - - - - - - - - - - - - - - - - - tgcattg