Sequence
atgc intronic sequence ATGC exonic sequencegtattttcccaaataaagttttttttcattccactattgatcttgctcaggactcaggagcagtaagaatacctttgtttaattataaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATAGTGATATTTGCAACAAATAGAGGTGTTTGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22330.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 7
---gtattttcccaaataaagttttttttcattccactattgatcttgctcaggact-caggagcagtaagaatacctttgtttaattataaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATAGTGATATTTGCAACAAATAGAGGTGTTTGCA
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tgtataacttatttattactattgttctactatatggtagaaatatgtcttaatgttgtttgatttaattacttattattgttaggaactttaattgcagGTCCACATGCTAGATATTGAATGCTTCTCTTATCTTAATCGTGCTCTGGAGAGCCCATTATCACCAATTGTGATACTTGCGACAAATAGAGGAATATGTA
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 7
gtattttcccaaataaagttttttttcattccactattgatcttgctcaggactcaggagca-gtaagaatacctttgtttaattataaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATAGTGATATTTGCAACAAATAGAGGTGTTTGCA
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------------gtgaccgtatctttaagtttctcaccgactaatgtctgcaaatactattgcatctaattaatcaaactttaatgcttttttacagGTTCATATGCTAGATATGGAGTGTTTTTCGTATTTGAATCGTGCTTTAGAGAGCTCCCTATCTCCAATAGTAATCTTTGCTACTAATAGAGGAATATGCA
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 7
gtattttcccaaataaagttttttttcattccactattgatcttgctcaggactcaggagcagtaagaatacctttgtttaattataaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATAGTGATATTTGCAACAAATAGAGGTGTTTGCA
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gtgactgtgtctttaaa-tttctcaccaactaatgtctgcaaatactattgcatctaatttatcaaaaaatttaatgtttttttg--------cagGTTCATATGCTAGATATGGAGTGTTTTTCGTATTTAAATCGTGCTTTAGAGAGCTCCCTATCTCCAATAGTAATCTTTGCTACTAATAGAGGAATATGCA
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 7
gtattttcccaaataaagttttttttcattccactattgatcttgctcaggactcaggagcagtaagaatacctttgtttaattataaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATAGTGATATTTGCAACAAATAGAGGTGTTTGCA
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gtctttttctcatttaa-tcccttttcatctttggatt-atctc-caaattgcttttgtgtatcttggatttctgaacttattttca------tagGTACACATGCTGGATATGGAGTGTTTTTCATATTTGAATCGTGCTCTAGAGAGCTCACTGTCTCCAATAGTAATTTTCGCTACAAATAGGGGAATATGTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116443984|gb|EG486576.1|EG486576EST: TAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG GTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAG
genomic: TAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAGgtattttccc ... aaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgctcaggactcaggagcagtaagaatacctttgtttaattataaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATAGTGATATTTGCAACAAATAGAGGTGTTTGCA
gtttaat putative branch site (score: 4)
taagaatacctttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttcccaaataaagttttttttcattccactattgatcttgctcaggactcaggagcagtaagaatacctttgtttaattataaaacctcagGTTCATATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATAGTGATATTTGCAACAAATAGAGGTGTTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA