Sequence
atgc intronic sequence ATGC exonic sequenceAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08850.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 5'ss of exon 2
AAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcag
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AAAACTGGCTGTGTGGCACTTGTGTTGTGTTTAAACATTAGTGTTGATCCGCCGGATGTGATCAAAATCTCCCCTTGTGCAAGAAAGGAGTGCTGGATAGgtaaacatttggtcatatctg--tatgcttgaattttagtgagctggaaaatttacatctgcctgcagct---ggcagttttatttc-atgtttatgggatgcaac-----
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 1
AAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcag
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--------------------------GTGTTTAAACATTAGTGTTGATCCGCCGGATGTGATCAAAATCTCCCCTTGTGCAAGAAAGGAGTGCTGGATAGgtaaacatttggtcatatgta--tatgcttgaattttagtcagctggaaaatttacgtctgcctgcagtt---ggcagttttatttc-atgtttatggtatgcaac-----
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 2
AAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcag
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AAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGATAGgtc----tctcgttacctttaatctcatt-tattttaatttttttatttctg---cagtttgtactctcaagagctttgtgtttcttaatagtattaaatgcttatat---
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G44210.1 (Glycine max), 5'ss of exon 2
AAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcag
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AAGACTGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCTCCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGATAGgtc----tcttgttacctttaatctcatttattttaatcttttttatttctgtagtttgtactctcaagaactttgcgtttcttaatagtattaaatgcttatt-------
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 5'ss of exon 2
AAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatct-ctattttttttctttctgatggcag--
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AAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGATAGgt----acattgatc------acactgcta-actctttcctatc-gtctttatttgttctgtagattg--atcataaactttttctattagtttttctgctgctaaatgctaacMapped 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|116460308|gb|EG502900.1|EG502900EST: GCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAG ATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATT
genomic: GCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactt ... ctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA