Sequence
atgc intronic sequence ATGC exonic sequencegtgattcacgaattcatcatctcctttttttagttttatatttccaaggtgttctcgggatatttcatgataaatgcatgaacacatgcatatttctgtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g54640.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g54640.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 8
gtgattcacgaattcatcatctcctttttttagttttatat-ttccaaggtgttctcgggatatttcatgataaatgcat--gaacacatgcatatttctgtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCA----
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gtgctttaagagtttatcatgtcctcaat--aattctatttattgccacattttctctatatttttta-gagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA
upper sequence: LOC_Os04g54640.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G004352_T02 (Zea mays), 3'ss of exon 8
gtgattcacgaattcatcatctcctttttttagttttatat-ttccaaggtgttctcgggatatttcatgataaatgcat--gaacacatgcatatttctgtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCA
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gtgctttaagagtttatcatgtcctcaat--aattctatttattgccacattttctctatatttttta-gagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAMapped 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|38476935|gb|CF961068.1|CF961068EST: TAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG AGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACA
genomic: TAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAGgtgattcacg ... gtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcgggatatttcatgataaatgcatgaacacatgcatatttctgtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCA
tttctgt CT-rich tract
atatttcatgataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattcacgaattcatcatctcctttttttagttttatatttccaaggtgttctcgggatatttcatgataaatgcatgaacacatgcatatttctgtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG