Sequence
atgc intronic sequence ATGC exonic sequence...gccattaacaagtggattagtctatattttagtggcttgtctttttcatattactcaattttcattttttctttaataaagttaatattttctcattcagGTTGGTGAGAGTGATGCTGTGATCATTATCACGCATGAACCCAACTGGCTTCTTGATTGGTACTGGAGCGGTGATACAGGGCAGAACGTGAGACATCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11800.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G135839_T01 (Zea mays), 3'ss of exon 10
gccattaacaagtggattagtctata----ttttagtggcttgtctttttcatattactcaattttcattttttctttaataaagttaatattttctc-attcagGTTGGTGAGAGTGATGCTGTGATCATTATCACGCATGAACCCAACTGGCTTCTTGATTGGTACTGGAGCGGTGATACAGGGCAGAACGTGAGACATCTGA
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--ctcttacggccttacctttccagaacatctcttggaacttggaagttgaaggtaat---atttacagatttaattgattgacttcaatactaaagctgtgcagGTTGGAGAGAATGATTCTGTGATTGTAGTAACACATGAGCCAAACTGGCTTCTTGATTGGTACTGGAATGAGACTACAGGCAAGAATGTATCACACTTAA
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 10
--gccattaacaagtggattagtctatattttagtggcttgtctttttcatattactcaattttcattttttctttaataaagttaatattttctcattcagGTTGGTGAGAGTGATGCTGTGATCATTATCACGCATGAACCCAACTGGCTTCTTGATTGGTACTGGAGCGGTGATACAGGGCAGAACGTGAGACATCTGA
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ggactcctacattattattctgttcttatttctgtttttcttcattcctaaattttctacttacggacttaacatc--ttcatctcatgatatttaactcagGTTGGAGAAAATGATTCTGTAATCATTATGACACATGAACCAAATTGGCTTCTGGATTGGTACTGGAATGATGTTTCTGGAAAAAATGTCTCACACCTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatattactcaattttcattttttctttaataaagttaatattttctcattcagGTTGGTGAGAGTGATGCTGTGATCATTATCACGCATGAACCCAACTGGCTTCTTGATTGGTACTGGAGCGGTGATACAGGGCAGAACGTGAGACATCTGA
agttaat putative branch site (score: 4)
ttttctcattc CT-rich tract
ttactcaattttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccattaacaagtggattagtctatattttagtggcttgtctttttcatattactcaattttcattttttctttaataaagttaatattttctcattcagGTTGGTGAGAGTGATGCTGTGATCATTATCACGCATGAACCCAACTGGCTTCTTGATTGGTACTGGAGCGGTGATACAGGGCAGAACGTGAGACATCTGA
- - -taacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaag