Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgatcattttggattctatttttttatttctatggctgccaatatgtttttcaattatttctatagagtaactgagctttctggtttcttatagTTTTCAAAAGAAAGGCGCAGCATATTTCCTGCTGGTGACACTTCTCAATTTATATCGTCAAAAGATGCTGACATTGCTATACTTGAAGAACCTGAACATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11670.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 4
gtatgttgatcattttggattctatttttttatt---tctatggc-tgccaatatgtttttcaattatttctatagagtaactgagctttctggtttcttatagTTTTCAAAAGAAAGGCGCAGCATATTTCCTGCTGGTGACACTTCTCAATTTATATCGTCAAAAGATGCTGACATTGCTATACTTGAAGAACCTGAACATC
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------------gtaagggttctcttttcataacaagtgaataaccttgcaacattgtgttca-ttacttgtctaatatcaattgtttgcaaagt-----atagTTTCAAAAAGAACGGAGAAGCATAATTCCTGCGGGGGACACTTCACAATTTATACCATCAAAGGAAGCTGACATTGCTATTTTGGAAGAGCCTGAGCACC
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 4
gtatgttgatcattttggattctatttttttatttctatggctgccaatatgtttttcaattatttctatagagtaactgagctttctggtttcttat----agTTTTCAAAAGAAAGGCGCAGCATATTTCCTGCTGGTGACACTTCTCAATTTATATCGTCAAAAGATGCTGACATTGCTATACTTGAAGAACCTGAACATC
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----gtaacttaatgagaaagttagctataatcctttatgtc-------atactttcatatcactactgtc-agttcttatgtttttgtcattctcatgtgtagTTTTCGGAAGCAAGGCGGAGTATAATACCTGCTGGAGATACTTCTCAATTTATACCATCCAGGGATGCTGACATTGCTATCCTGGAAGAACCAGAACATT
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 4
gtatgttgatcattttggattctatttttttatttctatggctgccaatatgtttttcaattatttctatagagtaactgagctttctggtttcttatagTTTTCAAAAGAAAGGCGCAGCATATTTCCTGCTGGTGACACTTCTCAATTTATATCGTCAAAAGATGCTGACATTGCTATACTTGAAGAACCTGAACATC
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--------gtaactttttggtaaagttagctatttcctttatgtttcatatcactactgtcggttcttacattttga---aattctcatgt-----gtagTTTTCGAAAGCAAGACGGAGTATAATACCTGCTGGAGATACTTCTCAATTTATACCATCCAGGGATGCTGACATTGCTATCCTGGAAGAACCAGAACATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatgtttttcaattatttctatagagtaactgagctttctggtttcttatagTTTTCAAAAGAAAGGCGCAGCATATTTCCTGCTGGTGACACTTCTCAATTTATATCGTCAAAAGATGCTGACATTGCTATACTTGAAGAACCTGAACATC
gagtaac putative branch site (score: 2)
ctttctggtttctt putative PPT
tgtttttcaattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgatcattttggattctatttttttatttctatggctgccaatatgtttttcaattatttctatagagtaactgagctttctggtttcttatagTTTTCAAAAGAAAGGCGCAGCATATTTCCTGCTGGTGACACTTCTCAATTTATATCGTCAAAAGATGCTGACATTGCTATACTTGAAGAACCTGAACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC