Sequence
atgc intronic sequence ATGC exonic sequence...atcttgaaggatagagcatactgtggtgctgcttttgaattttgatatgatagataaaaatctgatcttagaagatactttctactttgatttttttcagGATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATACAGTCTTTTAAGATCATGCACTATCGAACCAGAATGCATCATCGGGCAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48680.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g30460.1 (Oryza sativa), 3'ss of exon 1
------atcttgaaggatagagcatactgtggtgctgcttttgaattttgatatgatagataaaaatctgatcttagaagatactttctactttgatttttttcagGATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATACAGTCTTTTAAGATCATGCACTATCGAACCAGAATGCATCATCGGGCAACA
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acatgcccttttatgtatgtaac---ctgtaatatttgtgctaggtacttccataa---gccaaggtttcagttaatctcattcctaagttatgtattatgtgcagGACTACCAGCTGACACCCTTGTTGACCGGTATGTGACAGTGGGTGCATACTGTCTGTTGCGCTCATGCACTATTGAACCTGAGTGCATCATCGGTCAGCA
upper sequence: AT3G48680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g01240.t01 (Vitis vinifera), 3'ss of exon 1
atcttgaaggatagagcatactgtggtgctgcttttgaat--tttgatatgatagataaaaatctgatcttagaagatactttctactttgatttttttcagGATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATACAGTCTTTTAAGATCATGCACTATCGAACCAGAATGCATCATCGGGCAACA
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-aaataaatcat-gaacaaacccacaagcaaatcctgtatgatattatctgatctttactgaggacttttcagttgatactcaatttctttccatacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCAGTCTGTTGCGGTCTTGCACGATCGAACCTGAGTGCATTGTTGGGCAACAMapped 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|164208300|gb|ES170637.1|ES170637EST: TGTCCAGGAACGGTGTGTTGTTCATGCTGCGTGGTCGTCGCCTACAG GATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATAC
genomic: TGTCCAGGAACGGTGTGTTGTTCATGCTGCGTGGTCGTCGCCTACAGgttcttgttc ... tttttttcagGATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgatagataaaaatctgatcttagaagatactttctactttgatttttttcagGATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATACAGTCTTTTAAGATCATGCACTATCGAACCAGAATGCATCATCGGGCAACA
ctttctactttgattt CT-rich tract
tactttgattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcttgaaggatagagcatactgtggtgctgcttttgaattttgatatgatagataaaaatctgatcttagaagatactttctactttgatttttttcagGATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATACAGTCTTTTAAGATCATGCACTATCGAACCAGAATGCATCATCGGGCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagata