Sequence
atgc intronic sequence ATGC exonic sequence...tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 16
--------------------------------------------------------------------------------tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaattta---gaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
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gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgca-gtagtctgatag-atttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 1
tattggatctctaat-gatctg-catacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagc--gcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
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---atgatgtgcagtaggtctgatagagagttgtctttgactgtttatggaa-gtgacatttctctgatggtttgtgtgcactgttgcttacattcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTT
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 14
-------------------------------------------------------------tattggatctctaatgatctgcatacagttttaccttat---tttttgttgaacatgaattgagaatttag--aatta-ctaaggtcacagc-----gcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
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gtatatcatttcactgaggtctagtgttcatgatcatgctcgaacacggccttgtttcccgtaggaaagctataccagttcactgaggtttgaaagatatgagctgtctttgtttatgaatttggtgtctcgctgatgatctgtgttcgctgttgcttgcattcaatcacagGTTGTTCATGGATTTGGTCATGGAGTTCTGCGTAGGACGGACCCACGGTATCTATGCCAAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTT
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 15
tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatga-attgagaattt-----agaatt---actaaggtcacagcgcattc---atttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
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------------attaatatgcatatctgttcaccaaatgatgtagagagaatatcactgccaacttctcagataatataagctttggttgttgtgctttttggatttgcagGTTGTGCCTGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATT
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 15
tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaatt-gagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
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tttaatatacatatcttttcaccaaatgatttagagggaatattactgccaacttctcagataatataggctt-tggctgttgcactttttggatttgcagGTTGTGCCTGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATT
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
--tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
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tttccctaatatctcaccatct-catactaacgt-ttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTMapped 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|3758954|gb|C96653.1|C96653EST: CAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAAAG GTTGTTCCTGGCT-CGGTCATGGAGTTCTACGTAAGACCGAT
genomic: CAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAAAGgtagcttatc ... tcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
ttcattt CT-rich tract
aatttagaattactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT