Sequence
atgc intronic sequence ATGC exonic sequenceATATGAGCAACATTTACGTGCTATTCTTGGCCTTCCTCTTGGTGATCCTTCAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAGgtaactattgcaacactatctttttacttatccttgctatttgggccatgttgaatgtggataattaggtttccatattcctgttacattatccagttacctttattggcattgataatttatgatatag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10280.4 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G133121_T02 (Zea mays), 5'ss of exon 8
ATATGAGCAACATTTACGTGCTATTCTTGGCCTTCCTCTTGGTGATCCTTCAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAGgtaactattgcaacactatctttttacttatccttgctatttgggccatgttgaatgtg----------gataattaggtttccatattcctgttacattatccagttacctttattggcattgataatttatgatatag-------------------------
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ATATGAGCAGCATATACGCGCTATTCTTGGCCTTCCTCTTGGTGATCCCTCAATGAAAGCACCTGCAGCAATAATGTACAACATCCTGGGCGAGGATGAGgtaatgaatgctgt-tttcttctgtgcttatgattac-attttgaatatactgtatgcaataataggctgatggtcgggttttgttggcgtgcctccatgtttatattttagttattgtagtaattcagttagagtttaatatatcagacttgattgtgctgtag
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G36930.1 (Glycine max), 5'ss of exon 9
ATATGAGCAACATTTACGTGCTATTCTTGGCCTTCCTCTTGGTGATCCTTCAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAGgtaactattgca-acactatctttttacttatccttgctatttgggccatgttgaatgtggataattaggtttccatattcctgttacattatccagttacctttattggcattgataatttatgatatag
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ATATGAGCAACATTTGCGGGCTGTTGTTGGTCTTCCACTTGGTGATCCATCACTGAAAACTCCAGCTGCTATCATGTACAATATATTGGGTGAAGAAGAGgtactatcagcataaagtatttccccattttccattcctttcacctttgtcattaatctgaacaa--aagtctggttttctcccatacctgatgaggtgatg-----------------------------
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G30620.1 (Glycine max), 5'ss of exon 8
ATATGAGCAACATTTACGTGCTATTCTTGGCCTTCCTCTTGGTGATCCTTCAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAGgtaactattgca-acactatctttttactt---atccttgctatttgggccatgttgaatgtggataattaggtttccatattcctgttacattatccagttacctttattggcattgataatttatgatatag
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ATATGAGCAACATTTGCGGGCTGTTGTTGGTCTTCCACTTGGTGATCCATCACTGAAAACTCCAGCTGCTATCATGTACAATATATTAGGTGAAGAAGAGgtactatcagcatagagtatttccccattttccattcctttcaccttctttgtcattaatctgaaaaaaaagtctggttttctcctat-acgtgttgaggt---------------------------------
upper sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv14s0081g00240.t01 (Vitis vinifera), 5'ss of exon 9
ATATGAGCAACATTTACGTGCTATTCTTGGCCTTCCTCTTGGTGATCCTTCAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAGgta---actattgcaacactatctttttacttatccttgctatttgggccatgttgaatgtggataattaggtttccatattcctgttacattatccagttacctttattggcattgataatttatgatatag
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ATTCGAACAACATCTTCGGGCGGTTGTCGGCCTTCCTCTTGGTGATCCATCAATGAAAACCCCAGCTGCTATTATGTACAATTTACTGGGTGAAGATGAGgtacatacttttgttttccttttcttactcttttccaatctttatgagtcct-ttggatgtatggaattttgcctttccatgcttctgagagttttccttt--------------------------------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|58609163|gb|CK037196.1|CK037196EST: CAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAG GGTGAGGCAGGATTTACTCAAGCTCATCAGTTGATTGAGAGAGCTTTGGAC
genomic: CAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAGgtaactattg ... tatgatatagGGTGAGGCAGGATTTACTCAAGCTCATCAGTTGATTGAGAGAGCTTTGGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATATGAGCAACATTTACGTGCTATTCTTGGCCTTCCTCTTGGTGATCCTTCAATGAAAGCGCCTGCATCAATAATGTACAACATCCTGGGTGAGGATGAGgtaactattgcaacactatctttttacttatccttgctatttgggccatgttgaatgtggataattaggtttccatattcctgttacattatccagttacctttattggcattgataatttatgatatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG