Sequence
atgc intronic sequence ATGC exonic sequence...ctaatgaatgaaatttagtttcttgtttgtggatttttatatgttattagctggagaaggaccaatcgaatctgattgattttggctggaaattttttagGCGGTGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 1
ctaatgaatgaaatttagtttcttgtttgtggatttttatatgttattagctggagaaggaccaatcgaatctgattgattt--tggctggaaattttttagGCGGTGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA--
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--attggtctggctagtaggtgtcatgggtaaactaaagaatctcagt-gtaggtttcccattccttctatttagcttatttggtgacttggtatctacacag-
upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
----------ctaatgaatgaaatttagtttcttgtttgtg-----gatttttatatgttattagctggagaag-gaccaatcga------atctgattgat---tttggct---------ggaaattttttagGCGG-------TGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA
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gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 1
ctaatgaatgaaatttagtttcttgtttgtggatttttatatgttattagctggagaaggaccaatcgaatctgattgattttggctggaa---attttttagGCGG-------TGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA
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-------ctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagctggagaaggaccaatcgaatctgattgattttggctggaaattttttagGCGGTGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA
gattgat putative branch site (score: 4)
tttttt putative PPT
aaatttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaatgaatgaaatttagtttcttgtttgtggatttttatatgttattagctggagaaggaccaatcgaatctgattgattttggctggaaattttttagGCGGTGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - aatgaaa
- - - - - - - - - - - - - ttgtgga
- - - - - - - - - - - - - - - - - - - - - - - -tagctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctgg