Sequence
atgc intronic sequence ATGC exonic sequence...aatgcagcagttcctgcactgtggcactgaatttcctcaatgttcgaattattcttgtgcttatcattttctcttattgattataagtccactgttctagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g43590.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G070553_T01 (Zea mays), 3'ss of exon 9
aatgcagcagttcctgcactgtggcactgaatttcctcaatgttcgaattattcttgtgcttat-cat-tttctcttattgattataagtccactgttctagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
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-ttgagacatttctggttct-tcgtactaaaacccctcaaggatagaatccttaacttaattatgcacatttctttcattaattcagagttcattgttttagGGGTGCTGGACCTTCTCCAAGATCAAATCATGTAGCCGCCCTTTACGATGATAGAGTCCTATTGATTTTTGGAGGTCAGTCGAAGTCCAAGACCCTGAAT
upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G02680.1 (Glycine max), 3'ss of exon 7
-aatgcagcagttcctgcactgtggcactgaatttcctcaatgttcgaattattcttgtgct-tatcattttctcttattgattataag--tccactgttc-tagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
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gtaagtgattaaaaagaaaaagttggacttagttt---tgattatctagtcataatcacccaatatcctgatattatgtcgcctttgaaattgtattatttgcagGGGAACAGCACCTTCTCCAAGATTCAACCATGTAGCTGCTCTTTATGATGATAAAATTCTTTATATATTTGGAGGATCATCAAAATCCAGGACCTTAAAT
upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G38020.1 (Glycine max), 3'ss of exon 8
------------------aatgcagcagttc-ctgc-actgtggcactgaatttcctcaatgttcgaattattcttgtgct-tatcattttctcttattgattataagtccactgttct---agAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
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gtaagggattaaaaagaaaaagttggacttagttgtgattatctaatcataatcacccaatatcctgatttttttactgcaatatcctgatgttatgttgcctttgaaattatattacttgcagGGGAACAGCACCTTCTCCAAGATTCAACCATGTAGCTGCTCTTTATGATGATAAAATTCTTTATATATTTGGAGGATCATCAAAATCCAGGACCTTAAAT
upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G28760.1 (Glycine max), 3'ss of exon 7
--------aatgcagcagttcctgcactgtggcactgaatttcctcaatgttcgaattattcttgtgcttatcattttctcttattgattataagtccactgttctagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
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aaggacctgatttaaatgtttccttgcttttgtaatgtaatgct---gtgttc---tttttttttttacccccatactacctgctgaaatatcatatcactaac--agGGGAGCAGCACCTTGTCCTAGATTCAACCATGTGGCAGCTCTTTATGATGGTAAAATTCTATTTATATTTGGAGGAGCATCAAAATCCAGGACCTTGAAT
upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------aatgcagcagttcctgcactgtggcactgaatttcctcaatgttcgaattattcttgtgcttatcattttctcttattgattataagtccactgt-tctagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
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gtaagtgggtttcagtcaactgtattgaatttctcactaatatctttaaatattgtctttctactaaaatattttgaattttttttctttattatatgccatatctccttatgaactattatctaagatttggggttatgtatgtacagAGGAACGGGGCCCTCCCCAAGATCCAATCATGTGGCAGCTCTCTATGATGATAAAATTCTTTTTATTTTCGGAGGAGGATCAAAATCTAGGACTCTGAATMapped 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|25797320|gb|CA753281.1|CA753281EST: CTTCATATGTTTGACCTGAAATCTTCAACATGGCTTCCCTTGAATTATAA AGGTGCTGGACCTTCTCCAAGATCCATTCATGTGGCTGCTCTGTATGATGA
genomic: CTTCATATGTTTGACCTGAAATCTTCAACATGGCTTCCTTTGAATTATAAgtgagtcatc ... actgttctagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattattcttgtgcttatcattttctcttattgattataagtccactgttctagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
tattgat putative branch site (score: 3)
ctgttct putative PPT
attttctcttattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgcagcagttcctgcactgtggcactgaatttcctcaatgttcgaattattcttgtgcttatcattttctcttattgattataagtccactgttctagAGGTGCTGGACCTTCTCCAAGATCCAATCATGTGGCTGCTCTGTATGATGATAGAATTCTATTGATCTTTGGAGGCCAATCAAAATCCAAAACACTCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG