Sequence
atgc intronic sequence ATGC exonic sequencegtaatcattatagagatggttaaaccttgttatgctgacatatttaagtatagcattttcttgtttgtgtgattacttcgactgttgggttcaagcggtgatttcctttcagttgaatacagaacggaaatcacactgttattttacagcattgtatttttgtcaatgcagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCAAAATTCTCTCACAGGACAAGGAACATTTTGCAGAAATGGCCGTGGATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20890.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 7
gtaatcattatagagatggttaaaccttgttatgctgacatatttaagtatagcattttcttgtttgtgtgattacttcgactgttgggttcaagcggtgatttcctttcagttgaatacagaacggaaatcacactgttattttacagcattgtatttttgtcaatg--cagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCAAAATTCTCTCACAGGACAAGGAACATTTTGCAGAAATGGCCGTGGATGC
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-----------------------------------------------gtattgttgtttcatccccctttggataggaatatttcagggttgtatcattgtctctgtaaccttttaattcattgt-----tattactattatttaata-catta-atttactttaatgtccagAGAAATTCAGGTCAGACTTATTGAACATTGCAATGACTACTTTGAGCTCCAAGATTCTCTCACAGGACAAGGAGCATTTTGCAAAATTAGCTGTGGATGC
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 7
gtaatcattatagagatggttaaaccttgttatgctgacatatttaagtatagc-attttcttgtttgtgtgattacttcgactgttgggttcaagcggtgatttcctttcagttgaatacagaacggaaatcacactgttattttacagcattgtatttttgtcaatgcagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCAAAATTCTCTCACAGGACAAGGAACATTTTGCAGAAATGGCCGTGGATGC
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-----------------------------------------------gtattgttgtttctccccccttttggatacggatttttcagggttgtatcattg-ttctgtaaccttttaatacattgc-----tattactattatttaatacattaatttattttattgtccagAGAAATTCAGGTCAGACTTATTGAACATTGCAATGACTACTTTGAGCTCCAAGATTCTCTCACAGGACAAGGATCATTTTGCAAAATTAGCTGTGGATGC
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
gtaatcattatagagatggttaaaccttgttatgctgacatatttaagtatagcattttcttgtttgtgtgattacttcgactgttgggttcaagcggtgatttcctttcagttgaatacagaacggaaatcacactgttattttacagcattgtatttttgtcaatgcagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCAAAATTCTCTCACAGGACAAGGAACATTTTGCAGAAATGGCCGTGGATGC
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--------------------------------------------------------------------ctaaccatgttggtcat--gatatattatgtaatacttttccatctaatatttttccttaaattattatat-atctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGCMapped 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|125202219|gb|EL217173.1|EL217173EST: TGCTCGTAATGCTTTACTGAAAAGAGTCATTGATAACAAGGACAATGCAG AGAAGTTTAGGTCAGACTTGTTGA
genomic: TGCTCGTAATGCTTTACTGAAAAGAGTCATTGATAACAAGGACAATGCAGgtaatcatta ... gtcaatgcagAGAAGTTTAGGTCAGACTTGTTGA
EST:
gi|116444514|gb|EG487106.1|EG487106EST: TGCTCGTAATGCTTTACTGAAAAGAGTCATTGATAACAAGGACAATGCAG AGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCA
genomic: TGCTCGTAATGCTTTACTGAAAAGAGTCATTGATAACAAGGACAATGCAGgtaatcatta ... gtcaatgcagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacagaacggaaatcacactgttattttacagcattgtatttttgtcaatgcagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCAAAATTCTCTCACAGGACAAGGAACATTTTGCAGAAATGGCCGTGGATGC
tttttgtc CT-rich tract
attgtattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcattatagagatggttaaaccttgttatgctgacatatttaagtatagcattttcttgtttgtgtgattacttcgactgttgggttcaagcggtgatttcctttcagttgaatacagaacggaaatcacactgttattttacagcattgtatttttgtcaatgcagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCAAAATTCTCTCACAGGACAAGGAACATTTTGCAGAAATGGCCGTGGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA