Sequence
atgc intronic sequence ATGC exonic sequence...attagtagtagtagtaagggttatttttgtactgatatttttgctcactgtttcctaagagagtctgtccttctcataagggtttacttcttgattgcagTGCCATGGTTGGTTGCGGCAAACCCTGTCAATTATGGTCGTCCATGTGAATTGTCTTGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g09920.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g09920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G114758_T01 (Zea mays), 3'ss of exon 6
---attagtagtagtagtaagggttatttttgtactgatatttttgctcactgtttcctaagagagtctgtccttctcataagggtttacttct--tgattgcagTGCCATGGTTGGTTGCGGCAAACCCTGTCAATTATGGTCGTCCATGTGAATTGTCTTGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
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agaacctatgtaatgaagtaggtcctcttttatggcttcatatatgtaaactgg-----agttggatttgttaaatatatttgtgctttatttaaataattgcagTACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
upper sequence: LOC_Os03g09920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
attagtagtagtagtaagggttatttttgtactgatatttttgctcactgtttcctaag---agagtctgtccttctcataagggtttacttcttgattgcagTGCCATGGTTGGTTGCGGCAAACCCTGTCAATTATGGTCGTCCATGTGAATTGTCTTGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
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-agagtaat-gtgctcacctgtgatctcagaatggaattgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtgg-aattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactgtttcctaagagagtctgtccttctcataagggtttacttcttgattgcagTGCCATGGTTGGTTGCGGCAAACCCTGTCAATTATGGTCGTCCATGTGAATTGTCTTGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
tttacttctt CT-rich tract
tttactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attagtagtagtagtaagggttatttttgtactgatatttttgctcactgtttcctaagagagtctgtccttctcataagggtttacttcttgattgcagTGCCATGGTTGGTTGCGGCAAACCCTGTCAATTATGGTCGTCCATGTGAATTGTCTTGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG