Sequence
atgc intronic sequence ATGC exonic sequence...ttatgattttcctggattgtgtagttcatcagctagtcattatcttatggtaatgatatcaaacatgcagatatctcacgcaagaaattatttattacagGTAGTGGATGGAACATTCGTGGAAGAACCTGGGTCTGGTGCTGTAGCAACTGTTGAGAATAAAAAGGTTTCTGTTGGTACATTTGACTGGGTTCAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 3'ss of exon 12
ttatgatt--ttcctggattgtgtagttcatcagctagtcatt--atcttatggtaatgatatcaaacatgcagatatctcacgcaagaaattatttatt-acagGTAGTGGATGGAACATTCGTGGAAGAACCTGGGTCTGGTGCTGTAGCAACTGTTGAGAATAAAAAGGTTTCTGTTGGTACATTTGACTGGGTTCAAAG
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-tctaattagtatttctgttgcacaacactactatttcccatcgaagtttcaaattttactgttctatgtgttcattctttgcc----aatctatgcatttacagGCAAAAGATGGATCCTTCATGGAAGAACCTGGGTCTGGTGCTGTGGCGACCATTGGCGAGAAACAGGTTTCAGTTGGAACACTTGATTGGATCAGGAG
upper sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G24520.1 (Glycine max), 3'ss of exon 9
ttatgattttcctggattgtgtagttcatcagctagtcattatcttatggtaatgatatcaaacatg---cagatatctcacgcaagaaattatttattacagGTAGTGGATGGAACATTCGTGGAAGAACCTGGGTCTGGTGCTGTAGCAACTGTTGAGAATAAAAAGGTTTCTGTTGGTACATTTGACTGGGTTCAAAG
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taatgaatgta-tgtattttatatttca--agtgcattagcttcttgtcctgaaatttgagaagataaaactgctatcttatgcctcacggcataatttacagGTAAAAGATGGAACATTCCTGGAAGAACCTGGATCTGGTGCTGTGGCAACAATTGATAACAAAAAGGTTTCTGTTGGGACGTTGGAATGGATTACCAG
upper sequence: Vv12s0142g00330.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G07710.1 (Glycine max), 3'ss of exon 12
-ttatgattttcctggattgtgtagttcatcagctagtcattatcttatggtaatgatatcaaacatg---cagatatctcacgcaagaaattatttattacagGTAGTGGATGGAACATTCGTGGAAGAACCTGGGTCTGGTGCTGTAGCAACTGTTGAGAATAAAAAGGTTTCTGTTGGTACATTTGACTGGGTTCAAAG
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gttttaatgta--tgcattttacatttca--agtgcattagcttcttgtcctgaaatttgtgaagataaaactgctatcttatgccttacagcaaaatttacagGTAAAAGATGGAACATTCCTGGAAGAACCTGGATCTGGTGCTGTGGCAACAATTTATGACAAAAAGGTTTCTGTTGGGACATTAGAATGGATTACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggtaatgatatcaaacatgcagatatctcacgcaagaaattatttattacagGTAGTGGATGGAACATTCGTGGAAGAACCTGGGTCTGGTGCTGTAGCAACTGTTGAGAATAAAAAGGTTTCTGTTGGTACATTTGACTGGGTTCAAAG
atctcac putative branch site (score: 3)
aagaaattatttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgattttcctggattgtgtagttcatcagctagtcattatcttatggtaatgatatcaaacatgcagatatctcacgcaagaaattatttattacagGTAGTGGATGGAACATTCGTGGAAGAACCTGGGTCTGGTGCTGTAGCAACTGTTGAGAATAAAAAGGTTTCTGTTGGTACATTTGACTGGGTTCAAAG
- - - - ttcctgg
- - - - - - - - - - - - - catcagc
- - - - - - - - - - - - - - - - - - - - - -cttatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaat