Sequence
atgc intronic sequence ATGC exonic sequenceTGATACTCTTCAGAGTGAGGACAGTGGAATATTTGTTGGAGTCGAGGATGCAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcaccgaactattacagatcatgacaatttgaacttacacctatataatcttgtcagctacttatcatgtagttttatcagaagagctgaactgacatagactctttccag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g38440.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g38440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G149122_T01 (Zea mays), 5'ss of exon 9
--------------------------------------------------------------TGATACTCTTCAGAGTGAGGACAGTGGAATATTTGTTGGAGTCGAGGATGCAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcaccgaactattacagatcatgacaatttgaacttacacctatataatcttgtcagctacttatcatgtagttttatcagaagagctgaactgacatagactctttccag
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TGGAAGGCAATATCTCTGAGCATAGAGCTTAAAGTACAGCTTGCTGAAGAACAATCCCAAATTAACACCCTTCAGAGTGAGGACAGTGGGGTCTTTGTTGgtattgaggatgccaagagcctttagatgactgaagttttctcctcgaccatttcgaccaatgtaagttcaggcgacttgtatgg--ca----aatctaaatatac-------------------------------------------------------------------------
upper sequence: LOC_Os08g38440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G149122_T02 (Zea mays), 5'ss of exon 9
TGATACTCTTCAGAGTGAGGACAGTGGAATATTTGTTGGAGTCGAGGATGCAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcaccgaact---attacagatcatgaca---atttgaa--cttacacctatataatcttgtcagctacttatcatgtagttttatcagaagag-ctgaa-ctgacata-----gactctttccag
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TAACACCCTTCAGAGTGAGGACAGTGGGGTCTTTGTTGGTATTGAGGATGCCAAGAGCCTTTAGATGACTGAAGTTTTCTCCTCGACCATTTCGACCAATgtaagttcaggcgacttgtatggcaaatctaaatatacacttgcagtcctgcacttgtgcaagttcattaactacctatattgtggtcc-atcataagaggctgaaactgacattcatgtaactcttgctag
upper sequence: LOC_Os08g38440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G433609_T02 (Zea mays), 5'ss of exon 9
TGATACTCTTCAGAGTGAGGACAGTGGAATATTTGTTGGAGTCGAGGATGCAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcaccgaact---attacagatc---atg-acaatttgaa-cttacacctatataatcttgtcagctacttatcatgtagttttatcagaagagct--gaactgacataga-----ctctttccag
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TAACACCCTTCAGAGTGAGGACAGTGGGGTCTTTGTTGGTATTGAGGATGCCAAGAGCCTTCAGATGACTGAAGTTTTCTCCTCGACCATTTCGACCAATgtaagttcaggtgacttgtatggcaaatctaaatatacaattgcagtcctgcacttgtgcaagttcgttaactacctatattgtggtcc-atcataagaggttgaaactgacattcatgtatctcttgccag
upper sequence: LOC_Os08g38440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G379899_T01 (Zea mays), 5'ss of exon 6
TGATACTCTTCAGAGTGAGGACAGTGGAATATTTGTTGGAGTCGAGGATGCAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcaccgaact---attacagatcatgaca---atttgaa--cttacacctatataatcttgtcagctacttatcatgtagttttatcagaagag-ctgaa-ctgacataga-----ctctttccag
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TAACACCCTTCAGAGTGAGGACAATGGGGTCTTTGTTGGTATTGAGGATGCCAAGAGCCTTCAGATGACTGAAGTTTTCTCCTCGACCATTTCGACCAATgtaagttcaggcgacttgtatggcaaatctaaatatacacttgtagtcctgcacttgtgcaagtttattaactacctatattgtggtcc-atcataagaggctgaaactgacattcatgtatctcttgccag
upper sequence: LOC_Os08g38440.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179351_T01 (Zea mays), 5'ss of exon 8
TGATACTCTTCAGAGTGAGGACAGTGGAATATTTGTTGGAGTCGAGGATGCAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcaccgaact---attacagatcatgaca---atttgaa--cttacacctatataatcttgtcagctacttatcatgtagttttatcagaagag-ctgaa-ctgacataga-----ctctttccag
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TAACACCCTTCAGAGTGAGGACAGTGGGGTCTTTGTTGGTATTGAGGATGCCAAGAGCCTTCAGATGACTGAAGTTTTCTCCTCGACCATTTCGACCAATgtaagttcaggcgacttgtatggcaaatctaaatatacacttgcagtcctgcacttgtgcaagttcattaactacctatattgtggtcc-atcataagaggctgaaactgacattcatgtatctcttgccagMapped 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|27577936|gb|CB000631.1|CB000631EST: CAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAAT ATGGCCTCACTAATGGAAGTGTTTGG
genomic: CAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcac ... ctctttccagATGGCCTCACTAATGGAAGTGTTTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATACTCTTCAGAGTGAGGACAGTGGAATATTTGTTGGAGTCGAGGATGCAAAGAACCTTCAGATGAACGAGGTTTTCTCCTCCTCGATTTCTGCCAATgtaagttcaccgaactattacagatcatgacaatttgaacttacacctatataatcttgtcagctacttatcatgtagttttatcagaagagctgaactgacatagactctttccag
- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC