Sequence
atgc intronic sequence ATGC exonic sequence...ttagaattatggtctattagtagtctattcaattcatgagtgaataaacacccctaaagcttgggtcctaagttatattgtatcttctttgtgtgtgcagGTGGTTGTGGCGCTTGTGTTGTTCTTCTTTCAAAGTATGATCCATTGCTCGAAAAAGTCGATGAATTCACAATTAGCTCGTGTCTCACGCTTCTCTGTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20960.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 1
---ttagaattatggtctattagtagtctattcaattcatgagtgaataaacacccctaaagcttgggtcctaagttatattgtatcttctttgtgtgtgcagGTGGTTGTGGCGCTTGTGTTGTTCTTCTTTCAAAGTATGATCCATTGCTCGAAAAAGTCGATGAATTCACAATTAGCTCGTGTCTCACGCTTCTCTGTAG
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atagtttagccattgaagattatgattttgtctagcctatcaaaacctcaaaaatcaggtagctgatatattgatatgtttgccaacttcattgttt---cagGTGGTTGTGGTGCTTGTGTTGTTCTACTGTCCAAGTATAACCCTATACTTGACCAGTTGGATGATTGTACGGTGAGTTCATGTCTTACCCTGCTTTGTAG
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 1
-----ttagaattatggtctattagtagtctattcaattcatgagtgaataaacacccctaaagcttgggtcctaagttatattgtatcttctttgtgtgtgcagGTGGTTGTGGCGCTTGTGTTGTTCTTCTTTCAAAGTATGATCCATTGCTCGAAAAAGTCGATGAATTCACAATTAGCTCGTGTCTCACGCTTCTCTGTAG
| || || | || | | ||| | || | |||| | | | | || || | || ||| || || || | | ||||||| ||||| ||||||||||||||||| || |||||||| || |||| || | || ||||| || || | || || ||||| || || || || ||
ttgtttccaaaaaattttttacccattgaaaattttgt--atagcctatcaaaccctcaaagaatcaggtagctga--taccttg-atatttttgctaatttcagGTGGCTGTGGTGCTTGTGTTGTTCTTCTGTCCAAGTATGACCCTGTGCTTGACCAGGTGGATGATTTTGCAGTGAGTTCATGTCTTACACTGCTTTGCAG
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 1
---ttagaattatggtctattagtagtctattcaattcatgagtgaataaacacccctaaagcttgggtcctaagttatattgtatcttctttgtgtgtgcagGTGGTTGTGGCGCTTGTGTTGTTCTTCTTTCAAAGTATGATCCATTGCTCGAAAAAGTCGATGAATTCACAATTAGCTCGTGTCTCACGCTTCTCTGTAG
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atagtttagccattgaagattatgattttgtatagcctatcaaaatctcaaaaatcaggcagctgatacattgaaatgtttgctaacttcattgttt---cagGTGGTTGTGGTGCTTGTGTTGTTCTACTGTCCAAGTATAACCCTGTGCATGACCAGGTGGATGATTGTACGGTGAGTTCATGTCTTACCCTGCTTTGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacacccctaaagcttgggtcctaagttatattgtatcttctttgtgtgtgcagGTGGTTGTGGCGCTTGTGTTGTTCTTCTTTCAAAGTATGATCCATTGCTCGAAAAAGTCGATGAATTCACAATTAGCTCGTGTCTCACGCTTCTCTGTAG
ccctaaa putative branch site (score: 3)
tcttctttgt putative PPT
taagttatattgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagaattatggtctattagtagtctattcaattcatgagtgaataaacacccctaaagcttgggtcctaagttatattgtatcttctttgtgtgtgcagGTGGTTGTGGCGCTTGTGTTGTTCTTCTTTCAAAGTATGATCCATTGCTCGAAAAAGTCGATGAATTCACAATTAGCTCGTGTCTCACGCTTCTCTGTAG
- - - - - - - - - - - - - - -caattca
- - - - - - - - - - - - - - - - - - - - - - -aaacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaagc