Sequence
atgc intronic sequence ATGC exonic sequencegttcgtattggaattttgtgtagcttcttgttatattgcattggtgtcgcaattctgtgtgtacagtatttctccatttttctctctttgttcctggattttaagtttcatgtcacttttgtatggcagCACAGCATTCCTTATAGGCCCACAGCGGCAGGTGACTATGATGCTTGACCCAGCTCGTATCTACGCTACTGCATTGTATCTAGCAAGCATTATCATTGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23550.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G33260.1 (Glycine max), 3'ss of exon 3
gttcgtattggaattttgtgtagcttcttgttatattgcattggtgtcgcaattctgtgtgtacagtatttctccatttttctctctttgttcctggattttaagtttcatgtcacttttgtatggcagCACAGCATTCCTTATAGGCCCACAGCGGCAGGTGACTATGATGCTTGACCCAGCTCGTATCTACGCTACTGCATTGTATCTAGCAAGCATTATCATTGCC
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-----------------gaatagttc--tgttct----tatagaaatcgtttttaactgattaaactccttgtcatatgttctgttttcttc---aaatgctaagt---gggagtcttttttatggcagCACAGCATTCCTTATAGGTCCTAAAAGGCAAGTTACAATGATGCTTGACCCTGTTCGTATATATGCAACAGCCATATACATTGCAAGTATGATAATCGCC
upper sequence: AT5G23550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G28470.2 (Glycine max), 3'ss of exon 3
gttcgtattggaattttgtgtagcttcttgttatattgcattggtgtcgcaattctgtgtgtacagtatttctccatttttctctctttgttcctggattttaagtttcatgtcacttttgtatggcagCACAGCATTCCTTATAGGCCCACAGCGGCAGGTGACTATGATGCTTGACCCAGCTCGTATCTACGCTACTGCATTGTATCTAGCAAGCATTATCATTGCC
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---------aaaattatgaatagctccgtttttta----atagtattttaaactccttgt-catagctgttctgttttcttc-------------aaatgctaagtgggatttc--ttttttatggcagCACAGCATTCCTTATAGGTCCTAAAAGGCAAGTGACAATGATGCTGGATCCTGCCCGTATATATGCAACAGCCATATACATTGCAA--------------
upper sequence: AT5G23550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G28470.1 (Glycine max), 3'ss of exon 3
gttcgtattggaattttgtgtagcttcttgttatattgcattggtgtcgcaattctgtgtgtacagtatttctccatttttctctctttgttcctggattttaagtttcatgtcacttttgtatggcagCACAGCATTCCTTATAGGCCCACAGCGGCAGGTGACTATGATGCTTGACCCAGCTCGTATCTACGCTACTGCATTGTATCTAGCAAGCATTATCATTGCC
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---------aaaattatgaatagctccgtttttta----atagtattttaaactccttgt-catagctgttctgttttcttc-------------aaatgctaagtgggatttc--ttttttatggcagCACAGCATTCCTTATAGGTCCTAAAAGGCAAGTGACAATGATGCTGGATCCTGCCCGTATATATGCAACAGCCATATACATTGCAAGTATGATAATCGCC
upper sequence: AT5G23550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0130g00230.t01 (Vitis vinifera), 3'ss of exon 3
gttcgtattggaattttgtgtagcttcttgttatattgcattggtgtcgcaattctgtgtgtacagtatttctccatttttctctctttgttcctggattttaagtttcatgtcacttttgtatggcagCACAGCATTCCTTATAGGCCCACAGCGGCAGGTGACTATGATGCTTGACCCAGCTCGTATCTACGCTACTGCATTGTATCTAGCAAGCATTATCATTGCC
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---------------------agctttct----tctttcttttttgtactcattttctgtgggttttttttccctttttttttgggtgtatttc-agatgctaagttgga-gtg--ttttgtatggcagCACAGCATTCCTCATAGGCCCAAAACGGCAAGTGACCATGATGCTTGACCCTGTTCGTATTTATGCAACAGCCATATACCTTGCAAGTATAATAATTGCCMapped 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|125137491|gb|EL177346.1|EL177346EST: GTCAAGTTTGGCATCACATTCACTCTGGGAAATTTGATGGCACTCGGGAG CACAGCATTCCTTATAGGCC-ACAGCGG
genomic: GTCAAGTTTGGCATCACATTCACTCTGGGAAATTTGATGGCACTCGGGAGgttcgtattg ... tgtatggcagCACAGCATTCCTTATAGGCCCACAGCGG
EST:
gi|116474042|gb|EG516634.1|EG516634EST: GTCAAGTTTGGCATCACATTCACTCTGGGAAATTTGATGGCACTCGGGAG CACAGCATTCCT
genomic: GTCAAGTTTGGCATCACATTCACTCTGGGAAATTTGATGGCACTCGGGAGgttcgtattg ... tgtatggcagCACAGCATTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttttctctctttgttcctggattttaagtttcatgtcacttttgtatggcagCACAGCATTCCTTATAGGCCCACAGCGGCAGGTGACTATGATGCTTGACCCAGCTCGTATCTACGCTACTGCATTGTATCTAGCAAGCATTATCATTGCC
tcactttt CT-rich tract
attttaagtttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtattggaattttgtgtagcttcttgttatattgcattggtgtcgcaattctgtgtgtacagtatttctccatttttctctctttgttcctggattttaagtttcatgtcacttttgtatggcagCACAGCATTCCTTATAGGCCCACAGCGGCAGGTGACTATGATGCTTGACCCAGCTCGTATCTACGCTACTGCATTGTATCTAGCAAGCATTATCATTGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG