Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtttcatgggtctgctttgaaatctggttttatagtttatttggcttaaaggaatgattatgtttcatgggtctgctttgaaatctggtttttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50250.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G011129_T01 (Zea mays), 3'ss of exon 1
tgtgtttcatgggtctgctttgaaatctggttttatagtttatttggctt-aaaggaatgattatgtttcatgggtctgctttgaaatctggt-ttttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT
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--cattgtttgatcttttaggggtatatgttttcgtgttccccctgggttgaaaaaaaggagcttgctcatttgttctgaaatggactttgtcactgcgcagGTCATTTACAACAGAGAAACAGATCAAAGTCGTGGGTTTGGGTTTGTCACTATGAGCACTGTCGAGGAGGCTGAGAAGGCTGTGGAGATGTTCCATCGCT
upper sequence: AT5G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G36420.2 (Glycine max), 3'ss of exon 1
-----------tgtgtttcatgggtctgctttgaaatctggttttatagtttatttggcttaaaggaatgattatgtt----tcatgggtctgctttgaa-atctggttt--ttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT
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gtcagagagagagagagagagagaggctctttaccttctcgtgtttcaatttgaatttctgttaaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggttttagGTTATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTT
upper sequence: AT5G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G18470.1 (Glycine max), 3'ss of exon 1
---------------------------tgtgtttcatgggtctgctttgaaatctggtt--ttatagtttatttggcttaaa-----ggaatgattatgtttcatgggtctgctttgaaatctggtttttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT
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gtcagaaacaaagagagagaggctctttaccttctcgtgtttcaatttgaatttatgttaatgttattgtgttggggttgaaaacttgaaatgagcgtgcggtgtggttctttcttt---ttttgttattttagGTTATTTATAACAGGGAAACTGACCAGAGTCGCGGGTTTGGGTTTGTGACGATGAGTACTGTTGAAGAAGCTGAAAGCGCTGTGGAGAAATTCAACCGCT
upper sequence: AT5G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g09680.t01 (Vitis vinifera), 3'ss of exon 1
tgtgtttcatgggtctgctttgaaatctggttttatagtttatttggcttaaaggaatgattatgtttcatgggtctgctttgaaatctggtttttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT
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------gtatggagctgttcggt--ttggaatttgttgattttggggatttgggggtatatcatatct-gggtgtttgcttg----------ttttgcagGTTATTTACAATAGGGAGACTGATAGAAGTCGTGGGTTCGGGTTTGTGTCAATGAGTACTGTTGAAGAAGCCGAAAAGGCTGTGGATATGTTTCATCGTTMapped 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|124951879|gb|EL027204.1|EL027204EST: AAGCTTTAGCTATGCTCTTTGGACAAGCTGGTACTGTTGAGATTTCAGAG GTTATATACAATAGGGACACTGATCAAAGTCGTGGATTT
genomic: AAGCTTTAGCTATGCTCTTTGAACAAGCTGGTACTGTTGAGATTTCAGAGgtatatattg ... gtttttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcttaaaggaatgattatgtttcatgggtctgctttgaaatctggtttttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT
tttttgc CT-rich tract
aatgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtttcatgggtctgctttgaaatctggttttatagtttatttggcttaaaggaatgattatgtttcatgggtctgctttgaaatctggtttttgcagGTTATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - tgaaatc
- - - - - - - - - - - - - - ggtttta
- - - - - - - - - - - - - - - - - - - - tatttgg
- - - - - - - - - - - - - - - - - - - - - - - - - aaaggaat