Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatttctccttatatcgttgtacgatcttagatgatcgtgatgctatataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04140.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04140.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
------gtaaaatttctccttatatcgttgtacgatcttagatgatcgtgatgctatataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG
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catttggcattattacatcacagg-cattatacttttttggattgaagtcagattgtata---cttaatcagttagctgattca-atggaatttgccctt-----tgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
upper sequence: AT1G04140.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
---gtaaaatt-tctccttatat-cgttgtacgatcttagatgatcgtgatgctatataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG
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catttggcattattacattacaggcattatgcttttttggattgaagtcagattatata---cttaatcggttagctgactca-atggaatttgccctt-----tgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
upper sequence: AT1G04140.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaatttctccttatatcgttgtacgatcttagatgatcgtgatgctatataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG
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--atatcaagtatttgcatt-tcataaaatttctgcctagcctgtcatccttgatccttgttacttatggtttag-catatttatgacacaactgtgattccagTGAAATGGGTGCACATTTATCACCTTGTGGGAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATTTGGAAGCTGATCCTGGATTGCAAACACAGMapped 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|124921446|gb|EH995063.1|EH995063EST: CTGAAGTCTGACAAATGTCGATTAACAATACATCATGCTGTTCTTTGCAG TGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTT
genomic: CTGAAGTCTGACAAATGTCGATTAACAATACATCATGCTGTTCTTTGCAGgtaaaatttc ... atcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG
ttttgat putative branch site (score: 4)
atatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatttctccttatatcgttgtacgatcttagatgatcgtgatgctatataatatttctccttttgatggagatacatgatgtgtgtgtttatcgttgcagTGAGATGGGAGCCCATTTTTCTCCATGTGGGAGATATTTAGCAGCCTGTGTTGCATGCGTTATTCCTCATGCTGAGACAGATCCAAGTTTGCAGACACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG