Sequence
atgc intronic sequence ATGC exonic sequencegtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g16900.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 2
----------gtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
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gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgtttctatgatgtcttaatat-----ttttgttttgtgatttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG
upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 2
---------gtgccaagtgccttctgat-catgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
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tgttaattagtggatgaagttcattgatgcatgatatccgagaaggtagctcgtttctaca---atgtcttgacttaatatt--ttttttgctctgcgctttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG
upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 1
----gtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
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ttttgtttcttgttatgtagatttgtatattcatagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactgttgtaatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG
upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 1
----gtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
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gtttgttgcatgttatgtagatttgtatgttcatagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgctgttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG
upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------gtgccaagtgccttctgatcatgctttctgactatgta-gctcgttcttatgtatttattatatcttagtttgaacttttcctttt---gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
|| | | | | || | | | | |||| | | || | | ||| | || || | | |||| | ||| ||| | ||||| || | || || |||||||| || |||||||||||||||||||| || || | ||||| |||||| ||||||| |||| |||||||| | |
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggca-attttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ18109 (Selaginella moellendorffii), 3'ss of exon 2
---gtgccaagtgccttctgatcatgctttctgact------atgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
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tttgtgtttgccctcctttggctgcttttttcttctcaattcgcgcaacacagtgctaagagaacagtctttctcacttcgatagtttcttcatg----tgtagATTTTCAAGGCTGCGGGCGTTCCCATAGAATGGGAAGAACACTATGTTGGGACAACACTGGATCCCAAGACGGGAAGCTTTGTCACGTACGACAGCATGGMapped 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|58666245|gb|CK054931.1|CK054931EST: CTCTTCCGGCGATTGATGCAATGAAGTCACACCTTCTTGTTCCAAAAATG GTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
genomic: CTCTTCCGGCGATTGATGCAATGAAGTCACACCTTCTTGTTCCAAAAATGgtgccaagtg ... gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
cttttccttttgctgt CT-rich tract
ttatgtatttattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT