Sequence
atgc intronic sequence ATGC exonic sequence...ttaaaattcaatctcatttgtttatgctctcaaaattttgttgccttgagatgaatgtttttgatgatatgaatgtgaatcctctgttttgtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCATCGGAGCAAACAAAGCTCGAGAAGTTTCTTTAACATCGATGCCACTGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16210.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G033491_T01 (Zea mays), 3'ss of exon 1
--------ttaaaattcaatctcatttgtttatgctctcaaaattttgttgccttgagatgaatgtttttgatgatatgaatgtgaatcctctgttttgtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCATCGGAGCAAACAAAGCTCGAGAAGTTTCTTTAACATCGATGCCACTGACA
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tcagccaatacatttccactccaatttatttatgccgttg---ccttctaacctgttcacgt-catctgctgtgctctga---tcaatatccggtcttgtgat-gtagGTTTGGGATATTTCCTTCCTGGGGTCTTTCACAGAAGCTTTCTCGCATCATTGGGCCGAATAGAGCAAGGGAAGTGTCACTAACTTGCATGCCTGTTACT
upper sequence: AT4G16210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G03760.1 (Glycine max), 3'ss of exon 1
ttaaaattcaatctcatttgtttatgctctcaaaattttgttgccttgagatgaatgtttttgatgatatgaatgtgaatcctc----tgttttgtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCATCGGAGCAAACAAAGCTCGAGAAGTTTCTTTAACATCGATGCCACTGACA
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--agagtt--gttccacttatatacactattttgactatatcacaggatctccaacattattggatgtataattttctgttcttatagcatggtattgttgcagGTTTGGGATATTTCCTTCGTGGGGTTTGTCTCAGAAGCTTTCGCAGATCATAGGGGCCAATAAAGCCCGGGAGGTATCTCTCTCGGCCACACCTTTGACT
upper sequence: AT4G16210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0077g00860.t01 (Vitis vinifera), 3'ss of exon 1
ttaaaattcaatctcatttgtttatgctctcaaaattttgttgc----cttgagatgaatgtttttgatgatatgaatgtgaatcctctgttttgtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCATCGGAGCAAACAAAGCTCGAGAAGTTTCTTTAACATCGATGCCACTGACA
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-tggttttcagccatgaataaggatatgccttttgtctggatgtaaaattggtgatgtgggtgccttctgat---aatgtgtttagataaaactgttcttgcagGTTTGGGATATTTCCTTCATGGGGTCTCTCGCAGAAGCTCTCACGGATTATAGGAGCCAACAGAGCTCGTGAAGTGTCTTTAACAGCTATGCCTGTGACTMapped 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|86087219|gb|DR382978.1|DR382978EST: GATATTTTGGTCGCTTCTAGAGGAGCTAAGTTCATGGATACTCACGCCAG GTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCAT
genomic: GATATTTTGGTCGCTTCTAGAGGAGCTAAGTTCATGGATACTCACGCCAGgttgatttct ... gtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCAT
EST:
gi|86062053|gb|DR357810.1|DR357810EST: GATATTTTGGTCGCTTCTAGAGGAGCTAAGTTCATGGATACTCACGCCAG GTTTGGGATATTTCCTTCATGGGGNTTGTCTCAGAAGCTGTCCGAGGATCA
genomic: GATATTTTGGTCGCTTCTAGAGGAGCTAAGTTCATGGATACTCACGCCAGgttgatttct ... gtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTC-GAGGATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgagatgaatgtttttgatgatatgaatgtgaatcctctgttttgtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCATCGGAGCAAACAAAGCTCGAGAAGTTTCTTTAACATCGATGCCACTGACA
ttttgat putative branch site (score: 4)
aatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaaattcaatctcatttgtttatgctctcaaaattttgttgccttgagatgaatgtttttgatgatatgaatgtgaatcctctgttttgtgtttgaagGTTTGGGATATTTCCTTCATGGGGTTTGTCTCAGAAGCTGTCGAGGATCATCGGAGCAAACAAAGCTCGAGAAGTTTCTTTAACATCGATGCCACTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- -aaattca
- - - - - - - - - - - - - - ctcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - agatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttttg