Sequence
atgc intronic sequence ATGC exonic sequence...tgggcatacatagtagtagagcaacttctaagctctgaacactattactcagcagattgttcgtagggtttatgggtactaattcttctgttttgaacagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g66420.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g66420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G172001_T02 (Zea mays), 3'ss of exon 2
tgggcatacatagtagtagagcaacttctaagctctgaacactattactcagcagatt---gttcgtagggtttatgggtactaattcttctg-ttttgaacagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
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---gcgtggtctgcagt-gttttctgcttcagcctcgcactcttgtttgcagcagtgcccagttggtgtaacttgttatggctaattccattggttttgaacagAAAAGGAGAACTTGTGCCTTTATGGCTATCCCGATGAGACGTGGGAGGTGACCTTGCCAGCTGAGGAAGTTCCCCCTGAGATCCCTGAACCAGCATTAGG
upper sequence: LOC_Os01g66420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G080917_T02 (Zea mays), 3'ss of exon 2
tgggcatacatagtagtagagcaacttctaagctctgaacactattactcagcagattgttcgtagggt-ttatgggtactaattcttctg-ttttgaacagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
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agttcccagttggt-gtagaactagtacctagttttgatagttgctagatgatgctatgc-catatcttgttatggctactaattccattggttttgaacagAAAAGGAGAACTTGTGCCTCTATGGCTATCCCGATGAGACATGGGAGGTTACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTAGG
upper sequence: LOC_Os01g66420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
tgggcatacatagtagtagagcaacttctaagctctgaacactattactcagcagattgttcgtagggtttatgggtactaattcttctgttttga-acagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
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-tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgttatttgcaatgtgttttattaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
upper sequence: LOC_Os01g66420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G00630.1 (Glycine max), 3'ss of exon 2
tgggcatacatagtagtagagcaacttctaagctctgaacactattactcagcagattgttcgtagggtttatgggtactaattcttctgttttga-acagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
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-tgtccttcataatctcccaaataggaagaacccaaaagaatgattttttgaagtgttatttgcaatgtgttttgttaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
upper sequence: LOC_Os01g66420.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S117_107V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------tgggcatacatagtagtagag--caact---tctaagctctgaacactattactcagcagattgttcgtagggtttatgggtactaattcttctgttttgaacagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
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gttcgatttccgtgaacctaaacggtgttatcatatcgtgaaatgatgcattgttgactttggttgattgccacggttttggaaactgactgagtattagcagagatctttaacgctggatacgaccatagcaatccttgctgatggaaagt--tgtggaacgtgcagAAAAGGAAAACTTGTGTTTATACGGATACCCTGATGAATCATGGGAGGTTAACCTTCCAGCTGATGAAGTGCCCCCGGAGCTACCGGAGCCTGCGCTGGGMapped 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|33799651|gb|CF325688.1|CF325688EST: ATGTGGAGAAGTTTTACAAGCTCTGCGACCCTG AAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGA
genomic: ATGTGGAGAAGTTTTACAAGCTCTGCGACCCTGgtgagtgcgc ... ttttgaacagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactcagcagattgttcgtagggtttatgggtactaattcttctgttttgaacagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
tactaat putative branch site (score: 1)
ttcttctgtttt CT-rich tract
tactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggcatacatagtagtagagcaacttctaagctctgaacactattactcagcagattgttcgtagggtttatgggtactaattcttctgttttgaacagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- -gcataca
- - - - - - - - - - - - - - - - - ctgaaca
- - - - - - - - - - - - - - - - - - - - - - - - -cagcaga