Sequence
atgc intronic sequence ATGC exonic sequence...taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
taatagatgataaaaatgaaactctgtttcatatgaagtccca-agagtgtggtc-cagaata-attatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | | | | | ||| | || || | || || | ||||| | || || ||| || | ||||| | | | ||||||||| | |||||| || |||||||| ||||| || || || || |||||||| ||||||||||||||||| || || |||||||||||||| || ||||
gattctgttgttgtagtaaaattaaatta-atctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattca--tttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
taatagatgataaaaatgaaactct-gtttcatatgaagtcccaagagtgtggtccagaataatt-atgtct-tgcctcacatatagctat-tctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | | ||| || | | | | | | || || | | | | | | || |||| | | | ||| | | | | |||||| || | |||||| || ||||| || ||||| || || || || |||||||| |||||||||||||| || ||||| |||||||||||||| || ||||
----cggttttgaaattgtacttgtcgggttaaataaatgtgatgaacttttctacgttctggtttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtg----gtccagaataattatgtcttgcctcacatatagctattctaactc-tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | || | | ||| | | || | | | | || || || ||||| | | | | | | || | | ||||||||| ||||| ||||| ||||| || ||||||||||| || || ||||| || | |||||| || ||||| ||||| ||||| ||||| || ||||| |
-----ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
----taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactc-tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
|||| | ||| | | | ||| | | | ||| | | ||| || | || ||| | | ||||||||||||||| ||||||||||| |||| || || || || || ||||| ||||||||||| || ||||| |||| ||||| |||||||| |||||||
ccttccctagaccccacccatgcggaagcctctggcaccgggtct---gcccttttttcagta-atgtataatctgatt-gtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
-taatagatgataaaaatgaaac-tctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | ||| | || | | | |||| || | | | | | || ||| ||| | | || || | || ||||| || |||||| || |||||||||||||| | || || || |||||||||||||| |||||||| || | || |||||||||||||| |||||||
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaa--acagtaactaatcctttctgttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaact--ctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| || || | || || | || ||| | | | | || | || | | ||| | | | || | ||||||||| | ||||| || |||||||| ||||| || || || || |||||||| |||||||| ||||| || || || |||||||||||||| |||||||
gtttgaattatcatgattttttaaaacttgttttgtggtcatgtatatcttttttgtgctggtt-tacattat-taatatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 10
-----------------------------------------------------------taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtg-tggtccagaataat-tatgtcttgcctcacatatagctattctaactc--tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
|| | | || || | ||| |||| | | | ||| | | | | ||| || | || || |||| | | ||||||||||||||| || |||||||| |||| || || || || || ||||| ||||||||||| || ||||| |||| ||||| ||||| || ||||| |
gtacttttggatgctgatgtgttctttgtattttaaaacttgttactattgtaggtttatagtgtggtttttaagtggacatct-tttcgttttattatttggtggtgctcattttgtgtggcgtataatctgattgtgat-taattatttttggttggtcagAGCTTGAAGCATAATCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGTGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGGTCATTTGGAT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
--taatagatgataaaaatgaaactctgtttcata--tgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | | ||||| | || || | | || | ||| | | | | | || ||| || || | | |||| || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatt----tgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
-taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactct-cagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
|| || | ||||| | | || | | | | || | || | || || || | | | | | | | |||| || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgtttta--tgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
taatagatgataaaaatgaaactct--gtttca--tatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatat-agctattctaactctca-gAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| |||| ||| | | || |||| | ||| | | | | | || | || | | | || || || | | | || | | | |||| ||| || | |||||| || |||||||||||||| || || || || ||||| ||||| || || ||||||| |||||| |||||||||||||| ||||| |
-----taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgac-tggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagct-attctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | |||| ||| | || | || | | ||| | | | || || | | | || || || | | | | | | | |||||||| | | |||||| || ||||||||||| || || || || || ||||| || || || || |||||||||||||| |||||||||||||| ||||| |
agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgac-tggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaag--agtgtggtccaga---ataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | ||||| |||||| | | | || | ||| | | | | |||| |||| | | | | | || | | ||||||| | || || ||||| |||||||||||||| || || || || ||||| |||||||| || || || |||||||| ||||| ||||| |||||||| |
--gcattaagctaggatgaatgattgtttc-caccatattttaatttattgttatttatgtttacatttatttcttccttttttttt--tttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
taatagatgataaaaatgaaactc-tgtttcatatgaagtcccaagagtgtggtccagaataattatgtct--tgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
| | | || | | | | | || || | | || | | || | |||||| | || || | | | | | | | |||||| ||||||||||| ||||||| |||| ||| || || || || ||||| || |||||||| ||||| ||||||| |||||||||||||| ||||| |
-actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgtt--gtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcc---caagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
|| || | | || ||| || | | ||| | || ||| | |||| ||| | | | | | | | ||||||||| |||| || |||||||| || ||||| || || |||||||||||||||||||| || || ||||| |||| ||||| || ||||||||||| |
---gaggtgcttgaggtgtaacctggtcataattattgtctgtgcttgaaacatgtcaattataaatattcatggatgtgtgtgtttgtgtcttgttgtgcagAGCTTGGAGCATAATCCTAATGGCAGATTTGTGGTCGTATGCGGTGATGGAGAGTACATTATTTATACTGCCCTGGCATGGAGGAACAGATCTTTTGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
ttctaac putative branch site (score: 1)
ctattct CT-rich tract
aataattatgtctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA