Sequence
atgc intronic sequence ATGC exonic sequence...actattgaatttaagtgtgtttagatcattatgtacttcaataaataataaaaatcaagggtggtttgatgtcatgaaatatattgtgattattttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
Basic information
species | Glycine max |
transcript | GLYMA09G39270.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 4
--actat-tgaatttaagtgtgtttagatcattatgtacttcaataaataataaaaatcaagggtggtttgatgtcatgaaatatattgtgattattttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
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ttactatgtgtgattttgtgtatttactgtgcaatgcatttcagttattccgttaaagctgatata--taactgtccctttttcctttgggaaaaatt-gtagGTATTCAGTGGAAGATACTGGTCCTGTTACTTGTATATCTTGGACGCCTGACAATTGTGCTTTTGCAGTTGGATGGAAATTTAGGGGACTTACTGTGTGG
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 5
actattgaatttaagt-gtgtttagatcattatgtacttcaataaataataaaaatcaagggtggtttgatgtcatgaaatatattgtgattat-tttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
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-ttatacgcctttggtagttttcaagttgtcttactgtgatttatttcatgcccttgatattttggctg-catcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 5
actattgaatttaagt-gtgtttagatcattatgtacttcaataaataataaaaatcaagggtggtttgatgtcatgaaatatattgtgattat-tttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
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-ttatacgcccttggtagttttcaagttgtcttactgtgatttatttcatgcccttgatattttggctg-catcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
upper sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 5
actattgaatttaagtgtgtt-tagatcattatgtacttcaataaataataaaaatcaagggt----ggtttga-tgtcatgaaatatattgtgattattttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
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-----tggaacaatttccattgtacatcagaa-atggctagatgcatattgtcactaaatgctttttgtcttgactgtctttgtcttgctcctgtcttctgtgcagTTATTCAATGGACGATACTGGTCCGGTAAGTTGTATTGCATGGACGCCTGATAATTCCGCTTTTGCTGTTGGATGGAAGTTAAGAGGGCTTACAGTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taataaaaatcaagggtggtttgatgtcatgaaatatattgtgattattttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
gtttgat putative branch site (score: 5)
ttatttt putative PPT
atgaaatatattgtga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actattgaatttaagtgtgtttagatcattatgtacttcaataaataataaaaatcaagggtggtttgatgtcatgaaatatattgtgattattttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - gtgtgtt
- - - - - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtc