Sequence
atgc intronic sequence ATGC exonic sequencegtaaggaggaggaagaattttgaaacctttatttatacactttgaaatgtctaagtattttggtggtttcatactttgcagATTCACAAAGTCGACACGCTTGTCTCATACAAGAACGACGAGTGGGATGAAGAAGAGTAACAGAAGTCGGGACACACGTATGCAAGGCTCTTTGTTCAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g40940.2 (Oryza sativa), 3'ss of exon 4
gtaaggagga--ggaagaattttgaaacctttatttatacactt---tgaaatgtctaa--gtattttggtggtttcatactttg-cagATTCACAAAGTCGACACGCTTGTCTCATACAAGAACGACGAGTGGGATGAAGAAGAGTAAC-------AGAAGTCGGGACACACGTATGCAAGGCTCTTTGTTCAGC
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gtgaatatcactgaatcgactccgtttcttttttttcgctgcctctcccagattgctgacgttacagcgccgtgttcttgccatggcagATTCACAAGGTGGACACGCTCGTCTCCTACAAGGTCGACGAGTGGGACGAGGAGTAGAAGCCGCCGGTGGAGGTTGGAGC-CATGAGGAGGAGACCCCCTT------
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 6
gtaaggaggaggaagaattttgaaacctttattt-----atacactttgaaatgtctaagta-ttttggtggtttcatact-----ttgcagATTCACAAAGTCGACACGCTTGTCTCATACAAGAACGACGAGTGGGATGAAGAAGAGTAACAG---AAGTCGGGACACACGTATGCAAGGCTCTTTGTTCAGC
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gtgaatttggacttgcaatttggtttatttatctgactcacatactttgtttaattaagctaatactagtatttctgttctggctattgcagATTCACAAGGTTGACACACTTGTATCATACAAGAATGACGAATGGGATGAGCAGTAATGGCAGTCCGTGTCTTG-TATTTTTTTGTTCAGCTTCTTGCGTT--
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G01350.1 (Glycine max), 3'ss of exon 6
gt-aaggaggaggaagaattttgaaacc-tttattta------tacactttgaaatgtctaagta-ttttggtggtttcatactt-----tgcagATTCACAAAGTCGACACGCTTGTCTCATACAAGAACGACGAGTGGGATGAAGAAGAGTAACAGAAGTCGGGACACACGTATGCAAGGCTCTTTGTTCAGC
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gtgaatttggacttgtaatttttagttaatttatctaactcggcatactttgtttaatttagctaatactaatatttctgttttggctaatgcagATTCACAAGGTTGACACTCTTGTATCATACAAGAATGACGAATGGGATGAGCAGTAG-------------------------------------------
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0010g02430.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtaagga--ggaggaagaatt--ttgaaacctttatttatacactttgaaatgtctaagtattttggtggtttcatactttgcagATTCACAAAGTCGACACGCTTGTCTCATACAAGAACGACGAGTGGGATGAAGAAGAGTAACAGAAGTCGGGACACACGTATGCAAGGCTCTTTGTTCAGC--
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gtaagattatctcactaaatatttaaagcccagaacaagggttggttggatggatgattaatggtctttt-----tttgtttgttttgatggggccatg----gcagATACACAAGGTTGACACTCTTGTTTCATACAAGAACGATGAATGGGATGAGGATTAG-AAGAAATGAGGGGGCTCTTGT-TGCTATTCTTTTTCAGTTTCTAMapped 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|125232594|gb|EL246679.1|EL246679EST: AGTTGATTGCTAATCCACAGATGGTTAAGTTACACGGTTTTGATACCAAG ATTCACAAAGTCGACACGCTTGTCT
genomic: AGTTGATTGCTAATCCACAGATGGTTAAGTTACACGGTTTTGATACCAAGgtaaggagga ... tactttgcagATTCACAAAGTCGACACGCTTGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttatttatacactttgaaatgtctaagtattttggtggtttcatactttgcagATTCACAAAGTCGACACGCTTGTCTCATACAAGAACGACGAGTGGGATGAAGAAGAGTAACAGAAGTCGGGACACACGTATGCAAGGCTCTTTGTTCAGC
taagtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggaggaggaagaattttgaaacctttatttatacactttgaaatgtctaagtattttggtggtttcatactttgcagATTCACAAAGTCGACACGCTTGTCTCATACAAGAACGACGAGTGGGATGAAGAAGAGTAACAGAAGTCGGGACACACGTATGCAAGGCTCTTTGTTCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT