Sequence
atgc intronic sequence ATGC exonic sequencegtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79830.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 5
gtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
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-----------------------tacactttagagcccatttgattttttgcc---------cccttcatttttatgtttagtaggttttgaggcat------ttatttggcatcaacaatt--tttttacaatgaaca-----gGTGAAGAGCTATCAAAAAAACAAGCTGCTCAAGAAGCTACTATGCGGAAACTTAGGGCACAG
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G01980.2 (Glycine max), 3'ss of exon 6
gtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagc-ttgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
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------------------------------------gggcttttct-gttgtaattataaagtttctcca--------ttgaagcatggtagtggtttaattattggagattattgaggcccttatag-actgtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G43330.1 (Glycine max), 3'ss of exon 8
gtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagc-ttgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
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--------------------------------------ggtttttctgttgtaattaaatagtttctctattgaacc--------atggtagtggtttaattattggagattatagagacccttattagactgtctctcatctcagGTGAAGAGCTTTCCAAAAAACAGGCTGCTCAAGAATCCACAATTAGGAAACTAAGGGCTCAG
upper sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 5
gtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagct--tgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
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------------------------------------gtatgtatgtatgtatgtagga-----gttgatattgacca------aagggtaatgaggcccttcttttatatgctgataattttttaagatgcttgcctcttgcttcagGTGAAGAGCTTTCAAAAAAGCAAGCTGCTCAAGAGTCTCAGATTAGGAAATTAAGGGCACAGMapped 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|164158478|gb|ES159755.1|ES159755EST: AATCAAGTTATGGCTGAAG GCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGC
genomic: AATCAAGTTATGGCTGAAGgtaagacagc ... atcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
tgctaat putative branch site (score: 2)
tcatttc CT-rich tract
atattaatgctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacagccttttggaatgcttgaattatggatcgtatttttctcgttataaaaaaatggtgttgaaagcgaacacctgaaaaatgaaaggacgtcatttcttgctcagcttgagctcttgatattaatgctaatcatttcagGCGAAGAGCTTTCAAAGAAACAGGCTGCTCAAGAAGCTCAGATCAGGAAGCTAAGGGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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