Sequence
atgc intronic sequence ATGC exonic sequencegtatactttatcttattatcatcgtctctgaggtcagtgtcttccaggcagtcatggaagctagtgctaagcattttgacaactgttattgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G45850.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
----gtatacttt--atcttattatcatcgtctctgaggtca-gtgtcttccaggcagtcatggaagctagtgctaagcattttgac-aactgttattgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
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gtgagtaaacttaaaattttctattcattgattaaaatataatatatctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 4
-----gtatactttatcttattatcatcgtctctgaggtcagtgtcttccaggcagtcatggaagctagtgctaagcattt-tgacaactgtt----attgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
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gtgagttacttctaaatgtccaattatagataaaaaaatcaaatgcttctctctgatctttcaaattta-ataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 5
-----------gtatactttatcttattatcatcgtctc-tgaggtcagtgtcttccaggcagtcatggaagctagtgctaagcattttgacaactgttattgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
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acaacaaaagcatatgcataatatgaagttgtgtgttaggcaatgaaaagttcatttatcttcacataaaagtttgactgcaaaaattcaatgc------tttcagGGCAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACTCTTGGGCGTGTTATTAATGCGCTGGTTGAGCACTCTGGTCATGTTCCATATAG
upper sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S158_7V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatactttatcttattatcatcgtctctgaggtcagtgtcttccaggcagtcatggaagctagtgctaagcattttgacaactgttattgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
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gta-agtttctcttggtggt-tcattctgaagatt--tcctttgagaacagtccacacctcgaatttcactcactgtgattattgtcccttcagAATCGGGCTCGAGAAGCTGGAGAAATTAACAAAAGTCTTCTTACTCTTGGACGTGTCATTACTGCCCTTGTCGAACATCTAGGGCATGTACCCTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttccaggcagtcatggaagctagtgctaagcattttgacaactgttattgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
ttttgac putative branch site (score: 3)
attttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatactttatcttattatcatcgtctctgaggtcagtgtcttccaggcagtcatggaagctagtgctaagcattttgacaactgttattgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA