Sequence
atgc intronic sequence ATGC exonic sequence...actgaactccgttgtagcattagcgctgaaatgttctgtggttgaattaatttgtttctggcaaataattaaagttgttgctgttggatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14210.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 6
-----actgaactccgttgtagcattagcgctgaaatgttctgtggttgaattaatttgtttctggcaaataattaaagttgttgctgttggatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA
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gcaacgttaatgatagatcaatagatcatgccatggagcttttatgttg--tcaattgatgcctatttattattta---tcattgatcatgcgtgcatttaacagGAATATGGGCCATACTAAGAAACAATGAAATGCTAACTTGGCCAGAGAAGGTGAAGTTTGCTCTTGGACTTTTGCCAGCAATGGTTGGTGGCCAAGCTTA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G00720.2 (Glycine max), 3'ss of exon 1
ac-tgaactccgttgtagcattagcgctgaaatgttctgtggttgaattaatttgtttctggcaaataatta-aagttgttgctgttggatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA
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acatctgcatcattccccttttaagattctgttttattatgctttacgtt-ttaaatgttaaccagtatttacaagttgcatgccatgaatgtgaat-acagGAATATGGGCAATATTGAGGAACAATGAGATGCTTACATGGCCAGAGAAAGTAAAATTTGCAATTGGGCTTCTCCCAGCTATGCTTGGCGGACAGCCATA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 5
actgaactccgttgtagcattagcgctgaaatgttctgtggttgaattaatttgtttctggcaaataattaaagtt-----gttgc-tgttg-gatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA
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-------acatctgcatcattccccttttaagattctgtttcattatgctttactttctaaatgttaaccagtatttacgagttgcatgccatgaatgtcaatacagGAATATGGGCAATATTGAGGAACAATGAGATGCTGACCTGGCCAGAGAAAGTCAAATTTGCAATTGGGCTTCTACCAGCTATGCTTGGTGGACAGCCATA
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 6
actgaactccgttgtagcattagcgctgaaatgttctgtggt-tgaatta---atttgtttctggcaaataattaaagt-tgttgctgttggatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA
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-----tctttgtaattttctatgtttgtagattttttcctgtgtaaattatatattgctctccgcttgagttttaatgcatatttcttgtaaacatgattgacagGGATATGGGCCATCCTGAGGAATAATGAAATGCTGACTTGGCCGGAGAAAATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTAMapped 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|116473796|gb|EG516388.1|EG516388EST: AGAATTTAGTAGATTTGACTTCCCAGATGTCCTACCAGCACCCTTAAATG GTATTTGGGCTATTTTGCGGAACAACGAGATGCTG
genomic: AGAATTTAGTAGATTTGACTTCCCAGATGTCCTACCAGCACCCTTAAATGgtgagagaat ... tacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaatttgtttctggcaaataattaaagttgttgctgttggatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA
aattaat putative branch site (score: 3)
aaataattaaagttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgaactccgttgtagcattagcgctgaaatgttctgtggttgaattaatttgtttctggcaaataattaaagttgttgctgttggatttacgttgtagGTATTTGGGCTATTTTGCGGAACAACGAGATGCTGACATGGCCAGAGAAAATAAAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTA
- - - - - - - - - - - - -ctgaaat
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