Sequence
atgc intronic sequence ATGC exonic sequence...gtttagacttcttgagggatgatgattttactaacatggtcatgtagaaaatagactgttcatctagagaataaacagtttgcttgatgtgttaatgcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCCTTGTGACTCAGAAAAGGAAAATGTTCTTGCTGTTCAAGTGATGAGGTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g72340.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 4
gtttagacttcttgagggatgatgattttactaacatggtcatgtagaaaatagactgttcatctagagaataaacagtttgcttgatgtgttaatgcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCCTTGTGACTCAGAAAAGGAAAATGTTCTTGCTGTTCAAGTGATGAGGTGG
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gttggggcaggagtggagactggggggataataagatatccacattttgatagaaatcctgagatttattaacaaaacttgcaatattgtgtctgaacagTCAGGATAGTAGACTTCCTGCTGAATTTGAAATCACTGATTACTGTCATCCATGTGGTTCCAACAAGAAGAATGTTCTTGCTGTTCAAGTATTTAGATGG
upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ13378 (Selaginella moellendorffii), 3'ss of exon 4
gtttagacttcttgagggatgatgattttactaacatggtcatgtagaaaatagactgttcatctagagaataaacagtttgcttgatgtgttaat-gcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCCTTGTGACTCAGAAAAGGAAAATGTTCTTGCTGTTCAAGTGATGAGGTGG------------
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-----------------------------------------gtataaagtcttggtttcttaagtttcgggctgacag---acttggattgttacttgcagTCAGGACAGCCGTCTTCCATCCGAATTTGACATAACAAGCCTCTGCA------------CAGAAAAGGAAAATATTCTAGCTGTTCAAGTGATGCGATGGAGTGATGGATCG
upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ11904 (Selaginella moellendorffii), 3'ss of exon 4
gtttagacttcttgagggatgatgattttactaacatggtcatgtagaaaatagactgttcatctagagaataaacagtttgcttgatgtgttaat-gcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCCTTGTGACTCAGAAAAGGAAAATGTTCTTGCTGTTCAAGTGATGAGGTGG------------
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-----------------------------------------gtataaagtcttggtttcttaagtttcgggctgacag---acttggattgttacttgcagTCAGGACAGCCGTCTTCCATCCGAATTTGAGATAACAAGCCTCTGCA------------CAGAAAAGGAAAATATTCTAGCTGTTCAAGTGATGCGGTGGAGTGATGGATCGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29621652|gb|CB626663.1|CB626663EST: GTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAG CCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCC
genomic: GTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAGgtatggcaca ... gttaatgcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCC
EST:
gi|86904819|gb|CI310612.1|CI310612EST: GTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAG CCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCC
genomic: GTTGATTCAGCGTTTTTTGCTTGGGTAAACGGCGTTCCTGTTGGATATAGgtatggcaca ... gttaatgcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaaatagactgttcatctagagaataaacagtttgcttgatgtgttaatgcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCCTTGTGACTCAGAAAAGGAAAATGTTCTTGCTGTTCAAGTGATGAGGTGG
tgttaat putative branch site (score: 3)
agaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttagacttcttgagggatgatgattttactaacatggtcatgtagaaaatagactgttcatctagagaataaacagtttgcttgatgtgttaatgcagCCAGGACAGCAGGCTTCCTGCTGAGTTTGAGATCACAGATTTCTGCCATCCTTGTGACTCAGAAAAGGAAAATGTTCTTGCTGTTCAAGTGATGAGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT