Sequence
atgc intronic sequence ATGC exonic sequencegtatatatcaaatccttcaatgtttaatatataatcactcttttttgcagcagcaactgtttggttgatcattacaatgggatatatgaaagcaatacataaacattctgccttgttgacagagcaattatactgtattttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATAGGCAAATTAATGAGCTAAGGTCTGCAGTCAATGCTCATGCAGGTGATAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17260.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G030280_T01 (Zea mays), 3'ss of exon 6
gtatatatcaaatccttcaatgtttaatatataatcactcttttttgcagcagcaactgtttggttgatcattacaatgggatatatgaaagcaatacataaacattctgccttgttgacagagcaattatactgtattttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATAGGCAAATTAATGAGCTAAGGTCTGCAGTCAATGCTCATGCAGGTGATAA
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------------------------------gtaatcatcacttt--gcatgcataac-gtttgcttgctcactaccgtagaa-gcactcaggcagta-------attcttttttatggggaaaa---------tgcattttcttacagGGGCATTGGCCTTTGATATGGAGTATGCGAGGTGGTTGGAAGAGCACAATCGGCAAATTAGTGAACTAAGGGCTGGTGTCAGTGCTCATGCAAGTGATAC
upper sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G28400.2 (Glycine max), 3'ss of exon 3
gtatatatcaaatccttcaatgtttaatatataatcactcttttttgcagcagcaactgtttggttgatcattacaatgggatatatgaaagcaatacataaacattctgccttgt-tgacagagcaattatactgtattttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATAGGCAAATTAATGAGCTAAGGTCTGCAGTCAATGCTCATGCAGGTGATAA
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-----------------------------------caacatggtactcagtagca------tggatggtcatgggca-gggttttgcaaaag-------tttgtgctctgtttcaaatgctaaatcaatttaataatcttgttgtacagGCGCTATGGCATTTGATGTAGAGTACGCACGATGGTTAGAAGAGCATAATAGACAAACCAATGAGCTAAGGACTGCAATAAATTCTCATGCTGGAGATAT
upper sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G31050.3 (Glycine max), 3'ss of exon 9
gtatatatcaaatccttcaatgtttaatatataatcactcttttttgcagcagcaactgtttggttgatcattacaatgggatatatgaaagcaatacataaacattctgccttgttgacagagcaattatactgtattttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATAGGCAAATTAATGAGCTAAGGTCTGCAGTCAATGCTCATGCAGGTGATAA
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-----------------------------------caacatggtactcagtagca------tggatggtcatgggca-gggttttgaaaaagtt-----tgtgctttgtttcaaatcc-taaatcaatttaatcatcttgttatacagGCGCTATGGCATTTGATGTAGAGTACGCACGATGGTTAGAAGAGCATAATAGACAAACCAATGAGCTAAGGGCTGCAATAAATTCTCATGCTGGAGATAT
upper sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G28320.2 (Glycine max), 3'ss of exon 9
gtatatatcaaatccttcaatgtttaatatataatcactcttttttgcagcagcaactgtttggttgatcattacaatgggatatatgaaagcaatacataaacattctgccttgt-tgacagagcaattatactgtattttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATAGGCAAATTAATGAGCTAAGGTCTGCAGTCAATGCTCATGCAGGTGATAA
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-----------------------------------caacatggtactcagtagca------tggatggtcatgggca-gggttttgcaaaag-------tttgtgctctgtttcaaatcctaaatcaatttaataatcttgttgtacagGCGCTATGGCATTTGATGTAGAGTACGCACGATGGTTAGAAGAGCATAATAGACAAACCAATGAGCTAAGGGCTGCAATAAATTCTCATGCTGGAGATATMapped 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|88392088|gb|CI683916.1|CI683916EST: CATTTTTATATCCAGCTCAGTGGACCAGACTCATTCCATGAGTGGAAATG GGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATA
genomic: CATTTTTATATCCAGCTCAGTGGACCAGACTCATTCCATGAGTGGAAATGgtatatatca ... tttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATA
EST:
gi|88591033|gb|CI707939.1|CI707939EST: CATTTTTATATCCAGCTCAGTGGACCAGACTCATTCCATGAGTGGAAATG GGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATA
genomic: CATTTTTATATCCAGCTCAGTGGACCAGACTCATTCCATGAGTGGAAATGgtatatatca ... tttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATA
EST:
gi|88328466|gb|CI676674.1|CI676674EST: CATTTTTATATCCAGCTCAGTGGACCAGACTCATTCCATGAGTGGAAATG GGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATA
genomic: CATTTTTATATCCAGCTCAGTGGACCAGACTCATTCCATGAGTGGAAATGgtatatatca ... tttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatacataaacattctgccttgttgacagagcaattatactgtattttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATAGGCAAATTAATGAGCTAAGGTCTGCAGTCAATGCTCATGCAGGTGATAA
tgttgac putative branch site (score: 3)
tattttctt putative PPT
aattatactgtatttt 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 |
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gtatatatcaaatccttcaatgtttaatatataatcactcttttttgcagcagcaactgtttggttgatcattacaatgggatatatgaaagcaatacataaacattctgccttgttgacagagcaattatactgtattttcttgcagGGGCATTGGCTTTTGATATGGAGTATGCACGTTGGTTGGAAGAACACAATAGGCAAATTAATGAGCTAAGGTCTGCAGTCAATGCTCATGCAGGTGATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG