Sequence
atgc intronic sequence ATGC exonic sequencegtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G22780.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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gtaggcgctttttgctggatagtctg---tactacttctagccctcatttccatttatgtggtgctgaaatacttcaataaat---------------tgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g43730.1 (Oryza sativa), 3'ss of exon 9
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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---------------------------------gtaagagcacattccttttgcttttcttttctgtcattattgctcataacgttcttttt-catggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 8
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgc-acagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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-------------------gttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttat---aggtatta-attattatctttttgtagGATGACCCAAATAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G28740.2 (Glycine max), 3'ss of exon 4
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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------gtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaat-------------tctttttttcttgcagGATGACCTTAACAAAACTCCAGCCTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGCTATCAG
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgc-acagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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---------------------gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtatta-attattatctttttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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--gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttt-tcatatattaatt-----------attttttccttgca--gGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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------------------gttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgag---gttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAGMapped 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|164129394|gb|ES008315.1|ES008315EST: TTTGCTCCTAAAGTCATCAGAAATGCAGATTCCATCATGGAAGCTAGT GATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAAC
genomic: TTTGCTCCTAAAGTCATCAGAAATGCAGATTCCATCATGGAAGCTAGTgtaagagctc ... tcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAAC
EST:
gi|164100510|gb|ES118001.1|ES118001EST: CATTTGCTCCTAAAGTCATCAGAAATGCAGATTCCATCATGGAAGCTAGT GATGATGCCAGTAAAACCCCGGCTTC
genomic: CATTTGCTCCTAAAGTCATCAGAAATGCAGATTCCATCATGGAAGCTAGTgtaagagctc ... tcttgcacagGATGATGCCAGTAAAACCCCGGCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
cattaat putative branch site (score: 3)
ttatctt putative PPT
attaatctaa 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
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gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
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