Sequence
atgc intronic sequence ATGC exonic sequence...tactaagttcttctcatttctaatcagcagtactatatggtctgatagaggtgttagctcgttatgtatgataacttcatcttggtgatgaaatttatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09770.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G39250.1 (Glycine max), 3'ss of exon 3
tactaagttcttctcatttctaatcagcagtactatatggtctgatagaggt-gttagctcgttatgtatgataacttc--atcttggtgatgaaat-ttatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA
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-ccttgagaatgaacttgtctgg---gtagcctttttttttttaatttagcttgattgctcattgctggcattggcttataatttacattataaattattttagGGATCCCAACATGCTGCGAGACGTGCTGCTAGTTTTGTGCGAGGAGATGATGTCCTTCACAAGCTGTTTACAGAACTGGCTTATCGGTACAA
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 3
--tactaagttcttctcatttctaatcagcagtactatatggtctgatagaggtgttagctcgttatgtatgataacttc--atcttggtgatgaaat-ttatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA
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agaatgaactccttgtcat-----ggtagcccttttttcattttcatttagcttgattgctcattgctgggattggcctataatttacattataaattattttagGGATCCCAACATGCTGCAAGACAAGCTGCTAGTTTTGTGCGAGGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA
upper sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 3
tactaagttcttctcattt--ctaatcagcagtactatatggtctgatagaggtgttagctcgttatgtatgataacttcatcttggtgatgaaatt--tatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA
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---tgagtgcctagtgcttggtttttttctatttctttttcttcttggggacagctttgtttataaagaaaattatttttattcca-tcttgaaattattacagGGTTCTCTTTGTGCTGCAAGGCGTGCAGCAGCCTTTGTGCGAGGGGATGATGTGATTCACAAGCTATTCACTGAACTGGCTTATAGATACAAMapped 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|86077821|gb|DR373578.1|DR373578EST: TCGTCGTC-TGCTGATAATATGATTCAACTCGGCAAAGAG GGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGAT
genomic: TCGTCGTCTTGCTGATAATATGATTCAACTCGGCAAAGAGgtatttttat ... aaatttatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGAT
EST:
gi|19875182|gb|AU236013.1|AU236013EST: CTAAAGAGGTTCGTCGTCTTGCTGATAATATGATTCAACTCGGCAAAGAG GGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGAT
genomic: CTAAAGAGGTTCGTCGTCTTGCTGATAATATGATTCAACTCGGCAAAGAGgtatttttat ... aaatttatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaggtgttagctcgttatgtatgataacttcatcttggtgatgaaatttatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA
tgataac putative branch site (score: 2)
tgatgaaatttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactaagttcttctcatttctaatcagcagtactatatggtctgatagaggtgttagctcgttatgtatgataacttcatcttggtgatgaaatttatagGGGTCACTCTCTGCTGCAAGGCGAGCAGCTGGTTTTGTGAGAGGAGATGATGTCCTTCACAAGATTTTCACAGAACTGGCACATAGATACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - -cttctca