Sequence
atgc intronic sequence ATGC exonic sequencegtaagagcttaaagtttgttctctgaatgttctgtttatctttctgtttggagagatatatgttttcttaatatggaaaatcttcgaataagttgataaatgtaagttcattgatatggacagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTCTCTAAGTAGAAGTGGGATTCTCAGTCTAGATCGAGGAGATGCTGTAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16660.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G16070.1 (Glycine max), 3'ss of exon 4
gtaagagcttaaagttt------gttctctgaatgttctgtttatctttctgtttggagagatatatgttttcttaatatggaaaatct-tcgaataagttgataaatgtaagttcattgatatggacagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTCTCTAAGTAGAAGTGGGATTCTCAGTCTAGATCGAGGAGATGCTGTAATT
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gtaagcataaaaaaattcctgaagttttgttggcatattgcatatttaagccccttgaggaattgcttttcatgtaaaatttagaatctctagtgcccttctatttatgtttctcctctg-tacttctagATACTCATCTCGGAATCTGTCATCCCCCATCAAGGCAAACATTCATTTTTCTCTTAGTAGAAGTGGAATTCTTTCTCTGGATCGGGCAGATGCTGTTATT
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0043g00710.t01 (Vitis vinifera), 3'ss of exon 6
gtaagagcttaaagttt----gttctctgaatgttctgtttatctttc---tgtttggagagatatatgttttcttaatatgga--aaatcttcgaataagttgat-aaatgtaagttcattgatatgg---acagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTCTCTAAGTAGAAGTGGGATTCTCAGTCTAGATCGAGGAGATGCTGTAATT
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gtaaggatcaacaacttctacatgccatggagatttcagttttctttaatgctttttaaaacactgatgacctattcatctgcatgaaaccttcaaataaattggtcgaatttgaagtctttcttcttgtttgcagATACTCTTCTCGGAACCTGTCTTCTCCCATCAAGGCAAATCTGCATTTCTCTCTTAGTAGAAGTGGGATACTTTCTCTGGATCGAGCAGATGCTGTTACT
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g04410.t01 (Vitis vinifera), 3'ss of exon 5
gtaagagcttaaagttt----gttctctgaatgttctgtttatctttctgtttggagagatatatgttttcttaatatgga--aaatcttcgaataagttgat--aaatgtaagttc--attgatatggacagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTCTCTAAGTAGAAGTGGGATTCTCAGTCTAGATCGAGGAGATGCTGTAATT
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gtaaggatcaacaacttctagatgccatggagatttcagttttctttaatgctttttaaaca-atgatgacctattctgcatgaaaccttcaaacaaattggtcgaattctaagtccttatttttgtttgcagATATTCTTCTCGGAACCTGTCCTCTCCCATTAAGGCAAATCTGCATTTCTCTCTCAGTAGAAGTGGAATACTTTCTCTGGATCGAGCAGATGCTGTTATT
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0096g00090.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------gtaagagcttaaagtttgttc------tctgaatgttctgtttatctttctgtttgga-gagat------atatgttttcttaatatgga------------aaatcttcgaataagttgat-aaatgtaagttcattgatatgg---acagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTCTCTAAGTAGAAGTGGGATTCTCAGTCTAGATCGAGGAGATGCTGTAATT
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gtaaggatcaacaacttctagatgccatggagatttcagttttctttaatgctttttaaaacactgatgacctattcatctgcatgaaaccttcaaataaattggtcgaatttgaagtcatctgcatgaaaccttcaaataaattggtcgaatttgaagtctttcttcttgtttgcagATATTCTTCTCGGAACCTGTCCTCTCCCATCAAGGCAAATCTGCATTTCTCTCTTAGTAGAAGTGGGATACTTTCTCTGGATCGAGCAGATGCTGTTATTMapped 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|86060228|gb|DR355985.1|DR355985EST: CCTGTGTTTGCACAGTATTCTGTCTCTGGTTTGGCGGATGCATCTGAGAA ATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTC
genomic: CCTGTGTTTGCACAGTATTCTGTCTCTGGTTTGGCGGATGCATCTGAGAAgtaagagctt ... atatggacagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatatggaaaatcttcgaataagttgataaatgtaagttcattgatatggacagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTCTCTAAGTAGAAGTGGGATTCTCAGTCTAGATCGAGGAGATGCTGTAATT
aataagttgataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagcttaaagtttgttctctgaatgttctgtttatctttctgtttggagagatatatgttttcttaatatggaaaatcttcgaataagttgataaatgtaagttcattgatatggacagATATTCTTCTCGGAATCTATCAGCACCTATCAAGGCAAATCTGCATTTCTCTCTAAGTAGAAGTGGGATTCTCAGTCTAGATCGAGGAGATGCTGTAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG