Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttctcttccaccatcgtttttctttagttgttttaatctgctagttagtaatccactatttgacaaggttgaactgatttgttactgttgaaacactatgcagAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01230.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g49140.1 (Oryza sativa), 3'ss of exon 4
gtaagtttctcttccaccatcgtttttctttagttgttttaatctgctagttagtaatccactatttgacaaggttgaactgatttgttactgttgaaacactatgc-agAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
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gtaagtactagtttcagcgcgg-----cactgtctgttccagcagg---gttatgttcttagcatctga-----ttattttgcctcgttgtttatgggggattatactagAGAAGGTGACCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACA
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 5
gtaagtttctcttccaccatcgtttttctttagttgttttaatctgctagttagtaatccactatttgacaaggttgaactgatttgttactgttgaaacac-tatgcagAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
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------tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgt-attatctctctgtctctatcaatatcatcaatttcttgctgc---atcatgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G07970.3 (Glycine max), 3'ss of exon 4
gtaagtttctcttccaccatcgtttttctttagttgttttaatctgctagttagtaatccactatttgacaaggttgaactgatttgttactgttgaaacactatgcagAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
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--aattctttcttttattaaaaaaatgtgtc---ttattgaatcacttatattatctctctgtctctatcaatatc--atcaatttcttgctgc-gccatg-tatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAACGCTCGGACA
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtttctcttccaccatcgtttttctttagttgttttaatctgctagttagtaatccactatttgacaaggttgaactgatttgttactgttgaaacactatgcagAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
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---cgggcctcaagggcttctaattgttacta-ttatgtcaccctctttttgtgtaggaccttatt-gtcaagct---aataactttttact-taatcaaaattttcagGGATGGTGATCTTCCTCTTATTGTGGCGATTGATTTGCAGCCCATGGCTCCAATTGAAGGGGTGATTCAAGTCCAGGGTGATATAACAAATGCTCGTACAMapped 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|163971093|gb|ES011037.1|ES011037EST: GTCTTGAGTCGTCAATTATATCTTCCTGCAAAGTCCTCAGCTGAGTCAAA AGATGGGGATCTTCCTCTTA
genomic: GTCTTGAGTCGTCAATTATATCTTCCTGCAAAGTCCTCAGCTGAGTCAAAgtaagtttct ... cactatgcagAGATGGGGATCTTCCTCTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatccactatttgacaaggttgaactgatttgttactgttgaaacactatgcagAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
aactgat putative branch site (score: 3)
atttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttctcttccaccatcgtttttctttagttgttttaatctgctagttagtaatccactatttgacaaggttgaactgatttgttactgttgaaacactatgcagAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG