Sequence
atgc intronic sequence ATGC exonic sequence...aatgtttagtgagtgatatttatgaactgatcaatattgattaacttctcatcagcggtagatggaactctgagaacacatttttaatatgaaaacgcagGATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTGAGTAACTCAGGCAAACCGATATATTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28390.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G40080.2 (Glycine max), 3'ss of exon 2
aatgtttagtgagtgatatttatgaactgatcaatattgattaacttctcatcagcggtagatggaactctgagaacacattt--ttaatatg-aaaacgcagGATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTGAGTAACTCAGGCAAACCGATATATTCCAG
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-tgatacagacgtttattttttaaattcaagcaataagag--ggcattacactgaatatatgctgtaatatcatattctgtttgattaatgaataaagtgcagGATGATGCTTCCATTTCATGGAGGAAAAGGAAGAAGCATTTTTTTGTTCTGAGTAATTCTGGCAAACCAATATATTCTAG
upper sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 1
aatgtttagtgagtgatatttatgaactgatcaatattg-attaacttctcatcagcggtagatggaactctgagaacacattt--ttaatatg-aaaacgcagGATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTGAGTAACTCAGGCAAACCGATATATTCCAG
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-acgtttattttttaaattcaagcaatatgagggcattacactgaagat--atctgtaaaggctgtaa-tatcatattctgtttgattaatgaataaagtgcagGATGATGCTTCCATTTCATGGAGGAAAAGGAAGAAGCATTTTTTTGTTCTGAGTCATTCTGGCAAACCAATATATTCTAG
upper sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 1
aatgtttagtgagtgatatttatgaactgatcaatattgatt---aacttctcatcagc--ggtagatggaactctgagaacacattt--ttaatatg-aaaacgcagGATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTGAGTAACTCAGGCAAACCGATATATTCCAG
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-------tgcatataaccttcatttatttttctcagttgactcagaaaatacttttagtaagataaatggaa-tatcatgccctgtttgattaataaatgaagtgcagGACGATGCTTCTATTTCATGGAGGAAAAGAAAGAAGCACTTTTTCATTCTGAGTCACTCTGGGAAACCAATATATTCCAGMapped 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|19878055|gb|AU238886.1|AU238886EST: CCTCGCAGCATGAAGCTGCGTGGTTGCCTGGAAAACGCCATGTTGATGAG GATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTG
genomic: CCTCGCAGCATGAAGCTGCGTGGTTGCCTGGAAAACGCCATGTTGATGAGgttagtttga ... gaaaacgcagGATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcatcagcggtagatggaactctgagaacacatttttaatatgaaaacgcagGATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTGAGTAACTCAGGCAAACCGATATATTCCAG
ttttaat putative branch site (score: 3)
aacacatttttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgtttagtgagtgatatttatgaactgatcaatattgattaacttctcatcagcggtagatggaactctgagaacacatttttaatatgaaaacgcagGATGATGCTTCTACGTCATGGAGAAAGAGGAAGAAGCATTTCTTCATACTGAGTAACTCAGGCAAACCGATATATTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- tgtttag
- - - - - - - - - - - - - ctgatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaca