Sequence
atgc intronic sequence ATGC exonic sequencegtaaacttatgacttgaatgatctttgatcatagcgtcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattgctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21160.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
gtaaacttatgacttgaatgatctttgatcatagcgtcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctg-agatatagccttt-attgcta---ttttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
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---------------------------------------tgaac-tttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattacagacatggttttttgttgatataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
gtaaacttatgacttgaatgatctttgatcatagcgt-cgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattgctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
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---------------------------atcacactgtgcattccttctccagtgcatgtggatattta------tggtgcaatgatattga-tattatgaggtaatcactgaagatatgtacct--ttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 11
gtaaacttatgacttgaatgatctttgatcatagcg-tcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattgctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
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---------------------------atctcactgctcattccttctccagtgcatgtggatatttattttgcaacgatattgatat-------tatgaggtaatcactgaagatatgcacct--tactttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGAGAGAACTATTTCTTTCATTCTGGGCAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 6
gtaaacttatgacttgaatgatctttgatcatagcgtcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattg-----ctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
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---------------------------------------tgattccttctgccctccctgagttttctcttact-tttccagcatttggatgcttttcatgtggttcctatgagtgaattgcttggcctattttttgcagCTTGCCTGGACATGCTATAATTTCTACCAGTCAACACCAACAAAATTGGCTGGAGAGAACTATTTCTTCCACTCTGGGCAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 11
gtaaacttatgacttgaatgatctttgatcatagcgtcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattgctattttcc-----acatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
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---------------------------------------tgattccttctgccctccctgagttttctcttact-tttccaacatttggatgcttttcatgtggttcctatgagtgaattgcttgggatattttttgcagCTTGCCTGGACATGCTATAATTTCTACCAGTCAACACCAACAAAATTGGCTGGAGAGAACTATTTCTTCCACTCTGGGCAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 11
gtaaacttatgacttgaatgatctttgatcatagcgtcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattgctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
| | || | | | || ||| | || | || | |||||| || | || | || | ||| |||| ||| | || ||||||| ||||||||||||||||| ||||||||||| || | ||||||||||| ||||| ||||| || ||||
-------------------gtttcttataaaaaatattata----ctttaccagttgctcatggcttagatagtgctttgttgtctc---ttgtttgactagaatcttctttgc---cttctaa------tgtagCTTGCATGGACATGTTATAACTTCTACCAATCAACACCTATGAAACTGGCTGGAGAGAACTATTTTTTTTCTGCTGGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatttaggctgctgagatatagcctttattgctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
ttctgat putative branch site (score: 3)
tttattgctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacttatgacttgaatgatctttgatcatagcgtcgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattgctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA