Sequence
atgc intronic sequence ATGC exonic sequence...aaaatagattcaaattctctggggaaaagttataaaaatggattttttttgttatgaagtaataattgtggttttgattttttttgtgtgtgttttgcagTTATCAGCTTCAGAAATACAGAAATGCAGGTTCGTTTGTTCTTCCCGTTGATCCAAATGATAAGGAGACTTGGGGAGATAGTGAACACAGGTTAGCTTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60700.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G20460.1 (Glycine max), 3'ss of exon 1
aaaatagattcaaattctctggggaaaagttataaaaatggattttttttgttatgaagtaataattgtggttttgattttttt---tgtgtgtgttttgcagTTATCAGCTTCAGAAATACAGAAATGCAGGTTCGTTTGTTCTTCCCGTTGATCCAAATGATAAGGAGACTTGGGGAGATAGTGAACACAGGTTAGCTTAT
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---agccaccccagttcagtggctagcattttccctggcaccacttttatgttactgtattattatacttgctgaaaattctttgtttatttttttattgcagCTATCAGCTTCAGAAATACAAAAATGCTGGTTCATTTGTTCTTCCAGTGGATCCTAAGGACAAGGAAACATGGGGTGATAGTGAGCACAGGCTTGCATAT
upper sequence: AT5G60700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G08140.1 (Glycine max), 3'ss of exon 1
-aaaatagattcaaattctctggggaaaagttataaaaatggattttttttgttatgaagtaataattgtggttttgattttttttgtgtgtgtt-ttgcagTTATCAGCTTCAGAAATACAGAAATGCAGGTTCGTTTGTTCTTCCCGTTGATCCAAATGATAAGGAGACTTGGGGAGATAGTGAACACAGGTTAGCTTAT
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aagaagccaccccagttagtggctagcatttccttggcacca--cttttgtactactgtattattatacttactgaaaattctttactattttttattgcagCTATCAGCTTCAAAAGTACAAAAATGCTGGCTCATTTGTTCTTCCAGTGGATCCTAAGGACAAGGAAACTTGGGGTGATAGTGAACACAGGCTTGCATAT
upper sequence: AT5G60700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g02690.t01 (Vitis vinifera), 3'ss of exon 1
aaaatagattcaaattctctggggaaaagttataa-aaatggattttttttgttatgaagtaataattgtggttttgattttttttgtgtgtgttt-tgcagTTATCAGCTTCAGAAATACAGAAATGCAGGTTCGTTTGTTCTTCCCGTTGATCCAAATGATAAGGAGACTTGGGGAGATAGTGAACACAGGTTAGCTTAT
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--ctgatatttggatagtgacaggcagaatactgatgagtacttcctttatgactctaccttctgattctgcttctaatgattggaacctctaattgtgcagCTATCAGCTTCAGAAGTACAGAGATGCTGGCTCATTCGTTCTTCCTGTTGATCCAAATGACAAGGAAACTTGGGGTGACAGTGAACACAGGCTTGCTTATMapped 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|19877282|gb|AU238113.1|AU238113EST: TTCATCGAAAAACCATTCACATTCTCTACCGGNGAAGATCTTCATNTCAG TTATCAGCTTCAGAAATACAGAAATGCA
genomic: TTCATCGAAAAACCATTCACATTCTCTACCGGTGAAGATCTTCATCTCAGgttagtttcg ... tgttttgcagTTATCAGCTTCAGAAATACAGAAATGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgttatgaagtaataattgtggttttgattttttttgtgtgtgttttgcagTTATCAGCTTCAGAAATACAGAAATGCAGGTTCGTTTGTTCTTCCCGTTGATCCAAATGATAAGGAGACTTGGGGAGATAGTGAACACAGGTTAGCTTAT
ttttgat putative branch site (score: 4)
ttatgaagtaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaatagattcaaattctctggggaaaagttataaaaatggattttttttgttatgaagtaataattgtggttttgattttttttgtgtgtgttttgcagTTATCAGCTTCAGAAATACAGAAATGCAGGTTCGTTTGTTCTTCCCGTTGATCCAAATGATAAGGAGACTTGGGGAGATAGTGAACACAGGTTAGCTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
-aaataga
- - - - - caaattc
- - - - - - - - - - - ggaaaag
- - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagtaa