Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgttaagccttagaaattatgtaggccaatccctaatttctatttatgagaaaggaaaacccgttatcttttattatcaacgagcttgagaacgtgtagtagctagccttattatctgaaggctaatatcgctgaacaactatctattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAGACAATGGCTGATGTCTATGGTGCTTTCTATGATTTTTCCTGCATGCTGAAGACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34640.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 9
gtaagatgttaagccttagaaattatgtaggccaatccctaatttctatttatgagaaaggaaaacccgttatcttttatta-tcaacgagcttgagaacgtgtagtagctagccttattatctgaaggctaatatcgctgaacaactatctattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAGACAATGGCTGATGTCTATGGTGCTTTCTATGATTTTTCCTGCATGCTGAAGACAAAG
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---------------------------------------------------------tgttcatgtttgttgtctgctgttactctgtgtgtgtgttg-tgtgtaaatattaaactagctgtt--atttctgccttttgttttcacttttcaatt-tatagGTTTAACTGCCAAAGTGATTGACCGAACAAAGACTATGGCTGATGTCTACGGTGCTTTTTTTGATTTTGCTTCTATGTTGGAGCCCAAG
upper sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 9
gtaagatgttaagccttagaaattatgtaggccaatccctaatttctatttatgagaaaggaaaacccgttatcttttattatcaacgagcttgagaacgtgtagtagctagccttattatctgaaggctaatatcgctgaacaactatctattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAGACAATGGCTGATGTCTATGGTGCTTTCTATGATTTTTCCTGCATGCTGAAGACAAAG
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-------------------------------------------------------ggttttcgtgtttgttgtctgctgttgctc-tgtctgtgtgtgtgtgtaata-ctaaactagctgt-tatttcttcattttgttt--tcacttttcaatttatagGTTTAACTGCCAAAGTGATTGACCGAACTACGACTATGGCTGATGTCTATGGTGCTTTCTTTGATTTTGCTTCTATGTTGGAGTCCAAG
upper sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 9
gtaagatgttaagccttagaaattatgtaggccaatccctaatttctatttatgagaaaggaaaacccgttat--cttttattatcaacgagcttgagaacgtgtagtagctagccttattatctgaaggctaatatcgctgaacaactatctattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAGACAATGGCTGATGTCTATGGTGCTTTCTATGATTTTTCCTGCATGCTGAAGACAAAG
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--------------------------------------------------------gtcctttaccttgatataattttttttttgagcaaacagaatatgccgtgttaactggtgtt--taactctcggtccactttggtgg----tttgtttttttctagGTCTTACTGCCAAAGTTATTGACAGAACAAAAGCGATGTCTGATGTCTATGGTGCTTTCTTCGATTTTTCTTGTATGCTGAAGTCCAAGMapped 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|86078637|gb|DR374394.1|DR374394EST: TCAGAGGCGTTGTGAAACTGAGGCGAG GTCTTACTGCTAAAGTCATTGWTCGTACAAAGACAATGGCTGATGTCTATG
genomic: TCAGAGGCGTTGTGAAACTGAGGCGAGgtaagatgtt ... tattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAGACAATGGCTGATGTCTATG
EST:
gi|125227664|gb|EL241749.1|EL241749EST: ATGCTATAACAATGAACAAGTATTCAGAGGCGTTGTGAAACTGAGGCGAG GTCTTACTGCTAAAGTCATTGATCGTACAAAG
genomic: ATGCTATAACAATGAACAAGTATTCAGAGGCGTTGTGAAACTGAGGCGAGgtaagatgtt ... tattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagctagccttattatctgaaggctaatatcgctgaacaactatctattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAGACAATGGCTGATGTCTATGGTGCTTTCTATGATTTTTCCTGCATGCTGAAGACAAAG
ggctaat putative branch site (score: 3)
ttattatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgttaagccttagaaattatgtaggccaatccctaatttctatttatgagaaaggaaaacccgttatcttttattatcaacgagcttgagaacgtgtagtagctagccttattatctgaaggctaatatcgctgaacaactatctattgtttagGTCTTACTGCTAAAGTCATTGATCGTACAAAGACAATGGCTGATGTCTATGGTGCTTTCTATGATTTTTCCTGCATGCTGAAGACAAAG
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