Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 5
----gtaagttcttatgagcacggattgattgtcaaggactttctttttgtt-ctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
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gttgatactatgtttgctttttataccagtattctcagaattttttgatataacttttggcaagacatggta---aattttatcacttt-------tgcagACCATTTCAATATTTTTGTTGGTGATCTTAGCCCAGAGGTTACTGATTCCGCATTATTTGCATTCTTCTCTGGATATTCCAGTTGCTC
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
------gtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
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ataaaaataagcttaaacaaata-ggacctatgttcatactaagtctgatc-ccctttgggaacttttggctaaggtatagcctttttcttttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 5
--gtaagttcttatgagcacggattgattgtcaaggactttctttttgt--tctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
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aagcttaaacaaatgggccctatgttcatactaggcctgatcctttgggaacttttggctaagatattatattatatggcttgtttcctttaatttgcagGTCACTACAATATATTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGTTGTTTGCATGCTTTTCTGTCTATCCCAGTTGTTC
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
--------------gtaagttct---tatgagcacggattgattgtcaaggact--ttctttttgttctttgagtgaggcatggtactgaatg-gttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
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gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTCMapped 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|86052517|gb|DR348274.1|DR348274EST: TATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA GTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAG
genomic: TATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttctt ... tgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAG
EST:
gi|125018538|gb|EL090807.1|EL090807EST: TATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA GTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCA
genomic: TATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAAgtaagttctt ... tgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
atgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcttatgagcacggattgattgtcaaggactttctttttgttctttgagtgaggcatggtactgaatggttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT