Sequence
atgc intronic sequence ATGC exonic sequencegtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagtatgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtgaaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18100.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
gtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagta-tgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtgaaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC
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gtatgaaaa-----aacttcagaaattctgctggacgct--gaacatctgaactagtttctgtcgctcatattactc--taaacggttgatattctcttccaacttga-cagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 4
gtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagtatgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtg--aaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC
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-------gtatgaatacc-ttaacatcttttctgtgttctggaatat--atgatttcaaattggatgagtttccttgttgatttaattgtttttgtttttatgcatttaacagGATTAGCTGCCCCAGCAATTGCTGCAGGGCTTGGTGCTTTGGCTCCAACCTTGGGTACTCTGATCCCCGTAATTGGAGCAAGTGGATTTGCTGCAGCTGC
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G07870.1 (Glycine max), 3'ss of exon 3
gtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagtatgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtg--aaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC
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-------gtgtgaatacc-ttaacatcttttctgtgttctggaatat--ataatttcaaattggatgagtttccttgttgatttgattgtttttgtttttatgcatttaacagGATTAGCTGCCCCAGCAATTGCTGCAGGGCTTGGTGCTTTGGCTCCAACCTTGGGTACTCTGATTCCTGTAATTGGAGCAAATGAATTTGCTGCAGCTGC
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
---------gtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagtatgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtgaaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC
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gcaaccatagtaggacgtagtaaatatga-aatttctcttcaaaagcttcagacagcatgac--tgtttttg---------acttttcagttcatttt--tcac------tcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttggaaaatgctaattcttaatctgttttgattacatattatgtgaaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC
ttttgattacatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagtatgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtgaaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC