Sequence
atgc intronic sequence ATGC exonic sequence...attcaggttaagcctgcctcaatgggagatgtattagttgaaaaacatgagatgccagattttactggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16890.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g59630.1 (Oryza sativa), 3'ss of exon 2
attcaggttaagcctgcctcaatgggagatgtattagttgaaaaacatga--gatgccagattttactggtaatatatt--ttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
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---gtggctaggtttatttaca-gaaggatattgtcatgaaatttcttcacccaagtttatttgcaagaggacagtattgatattgttgttttgttggtgttagGAAGCTTTGAAATGGGTTACTGATCAACCTGCTTGGCAACGTTCAGAAGGCAGAGATCATGTAATTCCCGTTCATCACCCATGGTCGTTTAAGTCAGTTC
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G139691_T01 (Zea mays), 3'ss of exon 2
attcaggttaagcctgcctcaatggg-agatgtattagttgaaaaacatgagatgccagattttactggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
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-atcatttaagatctttatctctgtgtatggaaattactttattgttattcacttcaatttattccaagaggaacttatcatcattacatcttgatgttagGAAGCTTTGAAATGGGTCACAGATCAGCCTGCTTGGCAACGTTCAGAAGGCAGGGATCATGTCATTCCTGTTCATCATCCATGGTCATTTAAGTCAGTCC
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G02010.1 (Glycine max), 3'ss of exon 2
-attcaggttaagcctgcctcaatgggagatgtattagttgaaaaacatgagatgccagattttac-tggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
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gtttgttctttaattagtaacaacaattga-accttgtttttctgtttttcaatgactgctgtaatgtggacaattatgccttatgttgttgtggg-tgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G11550.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------------attcaggttaagcctgcctcaatgggagatgta-------ttagttgaaaaacatgagatgccagattttactggtaata--tattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
| |||| | | || | | || || || || || | ||| | | | | || ||| ||| | || | |||||||||||||||||||| |||||||||| ||||| |||||| | || | || || ||||||||| | || | |||||||| ||||| ||||||||||| |
gtgtgagtgctcttctaacgctctctgttctttgcttctacttctaaattaactattacagtgggaattggatcaaattgaggctttgttctttaattaattatttattaacaacacttttaaccttgcttttttcaatgactgctgtaatgtgatgtgaataattatgcttatgccttatgttgttgtggg-tgtagGAAGCTTTGAAGTGGATCACTGATCAACCTGCATGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTCAAGTCTGTTC
upper sequence: AT5G16890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0014g00560.t01 (Vitis vinifera), 3'ss of exon 2
attcaggttaagcctgcctcaatgggagatgtattagttgaaaaacatgagatgccagattttactggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
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atcacctatggggtaatcataaattagtttgtttctgagaatataattgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgagatgccagattttactggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
ttttaac putative branch site (score: 2)
ttttttaactcttttt CT-rich tract
attttactggtaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcaggttaagcctgcctcaatgggagatgtattagttgaaaaacatgagatgccagattttactggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
- - - - - - - - - - - - - - - - - - - -gaaaaac