Sequence
atgc intronic sequence ATGC exonic sequenceAAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAATTGAAGgttattttcagctcaattttgctctgtgcatagctacttaggttattttactaagtatttgaaataccacgcgtgtcaagtttgttccttttctgtagaagttctcaaggcctaactgtagaacccaattttgtgattgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g40740.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g40740.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 8
AAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAATTGAAGgttattttcagctcaattttgctctgtgcatagctacttaggttattttactaagtatttgaaataccacgcgtgtcaagtttgttccttttctgtagaagttctcaaggcctaactgtagaacccaattttgtgattgcag
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AAGGCTGGGATGCCGCCTGGTCCCAGAGCTGGTTTTTCAATGTGTGTGCACAAGAAAAGGGCTGTTCTTTTTGGTGGTGTGGTAGATATGGAAGTTGAAGgttact-----cataatcaagctctctgcac--ctgtgctacatgcttagctatatattagaaat-----gcatgtattttctgttgcttatgtttggtcatt--aaatgatta----------------------------
upper sequence: LOC_Os04g40740.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G36770.1 (Glycine max), 5'ss of exon 11
AAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAATTGAAGgttattttcagctcaattttgctctgtgcatagctacttaggttattttactaagtatttgaaataccacgcgtgtcaagtttgttccttttctgtagaagttctcaaggcctaactgtagaacccaattttgtgattgcag
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AAAAGTGGAATGCCTCCTGGTCCTCGTGCTGGGTTTTCCATGTGTGTTCATAAGAGAAGGGCTCTGCTATTTGGTGGTGTTGTGGATATAGAAGTTGAAGgttagctt-------------ttgtattcatgatta------ttatttttgcaa---tttgtgacac-----------agcttatatttttaaagcaagtgattggaaagtc-atctctatgacctaatgtt-tg-------Mapped 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|58657531|gb|CK046211.1|CK046211EST: AAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAACATTGAAG GGGATGTCATTATGAGCATGTTTATGAATGAGCTCTATGGTTTCCAGCTG
genomic: AAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAA-ATTGAAGgttattttca ... gtgattgcagGGGATGTCATTATGAGCATGTTTATGAATGAGCTCTATGGTTTCCAGCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAAACTGGGATGCCACCTGGCCCCAGAGCTGGGTTTTCTATGTGCGTTCACAAGAAAAGGGCTGTTCTTTTCGGTGGTGTGGTAGATATGGAAATTGAAGgttattttcagctcaattttgctctgtgcatagctacttaggttattttactaagtatttgaaataccacgcgtgtcaagtttgttccttttctgtagaagttctcaaggcctaactgtagaacccaattttgtgattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG