Sequence
atgc intronic sequence ATGC exonic sequenceGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50500.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 5'ss of exon 4
GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtac-gcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattt-tcctgtgaag-------------------
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GCTCGTTTCTTCTTCCAGCAGCTGATATCTGGAGTTAGCTACTGCCATTCCATGgtacagtatcattttgatttcaaagttaccgtgtgattttcgcttgtctataactataag-cggtttgctgcattgagctgaagcgattttgttaatgtgtttttgcattgttcag
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 4
GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagagcagtgttcttgc---aacttacttgaacttttctcgttctcgtgtataccac---tctggttttaattctgtgtttgattttcctgtgaag----------------
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GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATGgtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaag
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G06250.1 (Glycine max), 5'ss of exon 4
GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagagcagtgtt---cttgcaacttact------tgaacttttctcgttctcgtgtataccac---tctggttttaattctgtgtttgat-tttcctgtgaag--------------------------------------
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GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATGgta-actgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtgtcaatcttgagtattatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaag
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 4
GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagagcagtgttc---ttgcaacttacttgaacttttctcgttctcgtgtataccactctg-gttttaattctgtgtttgatttt-cctgtgaag-------------------------------------------------------
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GCTCGATTCTTCTTTCAGCAACTCATATCTGGGGTCAGCTATTGCCATGCTATGgta-attgaacattttccccttttctgttctatccaatctaaattgtgttt-tacacttcacactgcactgaaatgctgtaatatatgtaatgtattagtattaaacattatgtctgatgtatcagtcttgtttataatatgtctcttcataaag
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G09460.1 (Glycine max), 5'ss of exon 4
GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttt-taattctgtgtttgattttcc-tgtgaag----------------------------------------------------------------------
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GCTCGATTCTTCTTTCAGCAACTCATATCCGGGGTCAGCTATTGCCATGCTATGgta-attgaacattttcccctt--tctgctctgtccaatctaaattgagtttacactgcactgaaatgttgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaag
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 5'ss of exon 4
GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagagcagtgttcttgc-------aacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaag-----------
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GCTCGCTTTTTCTTTCAACAGCTTATATCAGGGGTCAGCTATTGTCATGCAATGgtatttgagcttttcttttttctgaaaaaaaaaatcttgaaaatttgtattcctttattctactaattccaattatataatttatctgacttttctatattcttttgatgaagMapped 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|164035085|gb|ES151173.1|ES151173EST: GGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG CAAATATGCCATCGGGATC
genomic: GGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagag ... tcctgtgaagCAAATATGCCATCGGGATC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaag
- - - - - - - - GCAGCT