Sequence
atgc intronic sequence ATGC exonic sequence...ttcataagcctggaaaatcttgttcgagaaaccaactgttaagttctcttttctttattgtataaacgattttcaattctaacacaaacgagttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08190.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08190.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g11880.1 (Oryza sativa), 3'ss of exon 7
ttcataagcctggaaaatcttgttcga-gaaaccaactgttaag--ttctcttttctttattg-tataaacgattttcaattctaacacaaacgag-ttat-ctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG
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------agcccatttttttaggaaggacgacctcagctattaagaaatctaaccacataatagctaggaacattattgaaattttgttcatgccatcttatgtcagGTGGGTTCGAGATACCTTGATCATTTGATAATTGAAAGAAAATATGCTGAAGCTGCACGCCTCTGTCCAAAATTGTTGCGAGGATCTCCTTCAGCATGGG
upper sequence: AT1G08190.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G08840.1 (Glycine max), 3'ss of exon 7
ttcataagcctggaaaatct-tgttcgagaaaccaactgttaagt---tctcttttctttattgtataaacgattttcaattctaacacaaacgagttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG
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aagatgtattttgtgtgtgtatatatgatttgtttccttctaggtgaatttttccatttgagtaatgagaagtttttcaatttgcccactatc----tttgcagGTGGGATCTAGGTACCTTGATCATTTGATTGTGGAAAGAAAATACAGGGAAGCAGCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGG
upper sequence: AT1G08190.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G19660.2 (Glycine max), 3'ss of exon 7
ttcataagcctggaaaatct-tgttcgagaaaccaactgttaagttctcttttc--tttattgtataaacgattttcaattctaacacaaacgagttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG
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aagatgtattttgtgtgtatatatatgctttgtttccttctaggttaatttgtccatttgagtaatgagaagtttttcatttttccc---actatctttgcagGTGGGATCTAGGTACCTTGATCATCTGATTGTGGAAAGAAAATACAGTGAAGCAGCATCTTTGTGTCCCAAGTTGCTTCGAGGATCAGCTTCAGCATGGG
upper sequence: AT1G08190.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0061g00940.t01 (Vitis vinifera), 3'ss of exon 7
ttcataagcctggaaaatct-tgttcgagaaaccaactgttaagtt--ctcttttctttattgtataaacgattttcaattc-taacacaaacgagttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG
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----agggcttaataattccatattttgatttccaatttttgtttagactgtttaatatattcaataacagagtatgctttcatcttgtcctctatatgcatagGTGGGATCAAGATACCTGGACCATTTGATTGTGGAAAGGAAATATGCTGAAGCTGCATCTTTGTGTCCTAAATTGTTGCGTGGATCTGCTTCAGCATGGGMapped 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|86063802|gb|DR359559.1|DR359559EST: CCCTAGCAGCTGTTGAGGCTAGTGAAGGACGAACCGAACTAATTGATAAG GTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAA
genomic: CCCTAGCAGCTGTTGAGGCTAGTGAAGGACGAACCGAACTAATTGATAAGgtactttttc ... agttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttttctttattgtataaacgattttcaattctaacacaaacgagttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG
ttctaac putative branch site (score: 1)
ttctttattgtataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcataagcctggaaaatcttgttcgagaaaccaactgttaagttctcttttctttattgtataaacgattttcaattctaacacaaacgagttatctagGTGGGAGCTGGGTATCTTGATCATTTGATTGTGGAAAGAAAATATGCTGAAGCGGCATCTTTATGCCCCAAATTGTTACGAGGATCTGCTTCAGCCTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- cataagc
- - - - - - gaaaatc
- - - - - - - - - - - - - - -aaccaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaaac