Sequence
atgc intronic sequence ATGC exonic sequence...tgtatcttgtaatctgatcgtcatatgaatctggttgtgtaagattcttggttgctcacaatgaaatctcattataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65430.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 8
tgtatcttgtaatctgatcgtcatatgaatctggttgtgtaagattcttg-gttgctcacaatgaaatctca-ttataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
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---------------gtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataa-cgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 8
tgtatcttgtaatc-tgatcgtcatatgaatctggttgtgtaagattcttggttgctcacaatgaaatctcattataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
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--------gtaagcattcttactttatgcattttattct-------tattagt-gcttgcaaatgaaacaaattg---atggctgcgctatcttactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 8
tgtatcttgtaatctgatcgtcatatgaatctggttgtgtaagattcttggttgctcacaatgaaatctcattataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
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----------------gtaggcattctttcttttatacattttattcttattagttt-tagcaaatggaaaacatga-tagttgtactatcatactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTG
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 8
tgtatcttgtaatctgatcgtcatatgaatctggt-tgtgtaagattcttggttgctcacaatgaa-atctcattataaatagttgtgttgtttaaatgt-agGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
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-------------------gtattgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
tgtatcttgtaatctgatcgtcatatgaatctggttgtgtaagattcttggttgctcacaatgaaatctcat-tataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
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gttatttttttttcaaattttaattcatatttagctttg-gagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttggttgctcacaatgaaatctcattataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
tgctcac putative branch site (score: 2)
aatgaaatctcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtatcttgtaatctgatcgtcatatgaatctggttgtgtaagattcttggttgctcacaatgaaatctcattataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaaa