Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtgaacgacttgctgttatccattagtattagatagttgagatacaaacaattttctaactattgacacatttcatctgcatgtgtaactcttgtagGCAGCGGTTACTTGACAGCTTGTTTTGCAATGATGGTTGGACCAGAAGGCCGTGCAGTGGGGATAGAACATATTCCTGAGCTTGTCGCTGCTTCGACTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g40540.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g40540.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G100315_T01 (Zea mays), 3'ss of exon 2
------------tgtgtgaacgacttgctgttatccattagtattagatagttgag-atacaaa-----caattttctaactat-tgacacatttcatc--tgcatgtgtaactc-ttgtagGCAGCGGTTACTTGACAGCTTGTTTTGCAATGATGGTTGGACCAGAAGGCCGTGCAGTGGGGATAGAACATATTCCTGAGCTTGTCGCTGCTTCGACTGA
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gtctgttgctgatacttcagccatttgcaagtgcccatcagcaattacaagctgaacaaacagcttgctcaaatttttttctgtctaactgatgccacaaatgcattcatgtcacgttatagGTAGTGGCTACCTGACAGCTTGTTTTGCCATGATGGTTGGACCAGAAGGCCGTGCAGTGGGAATTGAACACGTTCCCGAGATCGTTGCTTCTTCTGTTGA
upper sequence: LOC_Os04g40540.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 2
tgtgtgaacg---acttgctgttatccattagtattagatagttgagatacaaacaattttctaactattgacacatttcatctgcatgtgtaactcttgtagGCAGCGGTTACTTGACAGCTTGTTTTGCAATGATGGTTGGACCAGAAGGCCGTGCAGTGGGGATAGAACATATTCCTGAGCTTGTCGCTGCTTCGACTGA
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tacagaaatgcaaatcctctgcagtttctggattctgcatttctttgtgattaaagattctatattacctgac-cattttttttttttttttaaatttt--agGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTTGTGCAGTTGGAGTAGAACACATACCTGAGTTGGTTGCTTCTTCAATCAAMapped 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|218492459|gb|FG964268.1|FG964268EST: ACTGAAGGATCACTTGCAGCCAGGAATGCATGCTCTAGATGTTGGATCAG GCAGCGGTTACTTGACAGCTTGTTTTGCAATGATGGTTGGACCAGAAGGCC
genomic: ACTGAAGGATCACTTGCAGCCAGGAATGCATGCTCTAGATGTTGGATCAGgtattcaggt ... actcttgtagGCAGCGGTTACTTGACAGCTTGTTTTGCAATGATGGTTGGACCAGAAGGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaaacaattttctaactattgacacatttcatctgcatgtgtaactcttgtagGCAGCGGTTACTTGACAGCTTGTTTTGCAATGATGGTTGGACCAGAAGGCCGTGCAGTGGGGATAGAACATATTCCTGAGCTTGTCGCTGCTTCGACTGA
ctcttgt CT-rich tract
aattttctaactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtgaacgacttgctgttatccattagtattagatagttgagatacaaacaattttctaactattgacacatttcatctgcatgtgtaactcttgtagGCAGCGGTTACTTGACAGCTTGTTTTGCAATGATGGTTGGACCAGAAGGCCGTGCAGTGGGGATAGAACATATTCCTGAGCTTGTCGCTGCTTCGACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT