Sequence
atgc intronic sequence ATGC exonic sequence...acaccatttcaggctatactgttatgtttgaatttgtctaattattgcattagttctgttacttcaatatgaatatattgctgtggcttgtattttacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g47256.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g47256.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 7
acaccatttcaggctatactgttatgtttgaatttgtctaattattgcattagttctgttacttcaatatgaatatattgctgtggcttgtattttacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
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cgaacctctcagcttgtggaatgatactcagtctggcctgttttcttttggctttatctggttgttcttttactgtattgatgctgttcctattttcaagCTACTGGGAAAGCTGCCGAATTTGGACAGCTCAAAGATGGTTATATGTTCGACACATCAACTGGCATGTCACGAAT
upper sequence: LOC_Os01g47256.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 7
acaccatttcaggctatactgttatgtttgaatttgtctaattattgcattagttctgttacttcaatatgaatatattg-ctgtggcttgtattttacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
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-gaacctctcagcttgtcgaatgatactctgtctggcctgttttcttttggctttgtctgattgttcttttactgtattgattgctgttcctattttcaagCTACTGGGAAAGCTGCCAAATTTGGACAGCTGAAAGATGGTTATATGTTCGACACATCAACTGGCATGTCACGAAT
upper sequence: LOC_Os01g47256.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------acaccatttcaggctatactgttatgtttgaatttgt-ctaattattgcattagttctgttacttcaatatgaatata---ttgctgtg-gcttgtattttaca-gCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
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gtaattttttagcttgcagctcagtgtctactttccttaattttctatcagaagtatggaataccaaatgttctagcatatgtaacctcattgcttgtgagatgatactcagtatggatcgtttgtttttggttttatctgattgttctttttccgtatgttcctatttttcaagCTACTGGGAAAGCTGCTGAATTTGGTCAGCTGAAAGATGGTTATATGTTTGACACATCAACTGGCATGTCAAGAAT
upper sequence: LOC_Os01g47256.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G06540.1 (Glycine max), 3'ss of exon 8
--------------------------------------acaccatttcaggctatactgttat-gtttgaatttgtctaattattgcattagttctgttacttcaatatgaatatattgctgtggcttg-tattt-tacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
|| ||| || | | | || | |||| ||| | | ||| ||| || || || | || | || ||| | ||| | ||| | ||||||||| || ||||||||| ||||||||||||||||||||||| | || || | || ||||
gtaggtgttttatcttttttgtttttctgtgcctcttaacttaattatagattttttttttgttgtttacgtttaaatt-tgtttgttttatttttgcagacctaaccctgcc-ttttattttgttttggtgtttgtttagCCAGTGGGAAAGCTGCAGAATTTGGTGCCCTAAAAGATGGCTATATGTTTGAGTGTACAACAGGTCAATCAAGGAT
upper sequence: LOC_Os01g47256.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G12480.1 (Glycine max), 3'ss of exon 7
----------------------------------------------acaccatttcaggctatactgttatgtttgaatttgtctaattattgcattagttctgttacttcaatatgaatatattgctgtggcttgtattttacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
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gtaggtgtttgttctcgacctcattttaagttcttattttctgtgcctatcaattataggttttttgt--tggttaagttaaatttatttctattttatttttgctgacttgactcttttattttgtttcggtgtttgttt---agCCAGTGGGAAAGCAGCAGAATTTGGTGCCCTAAAAGATGGCTATATGTTTGAGTGTACAACGGGTCTCTCAAGGATMapped 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|58653630|gb|CK042310.1|CK042310EST: AGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATG CTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTG
genomic: AGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATGgtaaaactat ... tattttacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcattagttctgttacttcaatatgaatatattgctgtggcttgtattttacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
ttacttcaatatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaccatttcaggctatactgttatgtttgaatttgtctaattattgcattagttctgttacttcaatatgaatatattgctgtggcttgtattttacagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCCTGTCGCGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG