Sequence
atgc intronic sequence ATGC exonic sequenceACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacatcaaagaactagatgatataaagcatgatcgacctgcatttgtttagtctaggtacttgcttttcttggatgcaaacaatagtaatttgaa...
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 12
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattaca-tcaaagaacta-----gatgatataaagcatgatcg-------acctgcatttgtttagtctaggtacttgcttttcttggatgcaaacaatagtaatttgaa--------------------------------------------------
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ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGGCCCATGAAGCAGAGgtaattacaatcatttaattatgtcagatgctacaatgcatgatagttatgttatacgcgctgcatttctctagcaatacaaagctttgtaaacatgatcattgagatgtgatgaactattgttgctaagctttgttatcaacatctgttgcttgtttcttag
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G082099_T01 (Zea mays), 5'ss of exon 6
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacatcaaagaactagatgatataaagcatgatcgacctgcatttgtttagtc-taggtacttgcttttcttggatgcaaacaatagtaatttgaa------
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ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCGAGGTGGCCCATCAAGCAGAGgtaattac----aatcatttaattatatcagatgcta-caatgcatgatagttatgttatacgcgctgcatatgctacaatgc--atgatagttatgttatacgtgc
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G480263_T01 (Zea mays), 5'ss of exon 8
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattaca-tcaaagaacta-----gatgatataaagcatgatcg-------acctgcatttgtttagtctaggtacttgcttttcttggatgcaaacaatagtaatttgaa--------------------------------------------------
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ATCTAGAAGAAGTTGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGTGGCCCATGAAGCAGAGgtaattacaatcatttaattatatcagatgctacaatgcatgatagttatgttatacgcactgcatttctgtagcaatacaaagctttgtaaacataatcattgagatgtgatgaactattgttgctaagctttgttatcaacatccgttgcttgtttcttag
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G164265_T02 (Zea mays), 5'ss of exon 12
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattaca-tcaaagaactagatgatataaagcatgatcgacc---tgcatttgtt----tagtctaggtacttgcttttct-tggatgcaaacaatagtaatt--tgaa--------------------------------------------
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CAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTTATAATGCTAGGCGACCCATGAAGCAGAGgtatttacaatcatttaattagatgctacaaggcatgatagtttggttacacttgctgcatttctctagtaacacgtagccctgtaaacatgatcattaagatgtgatgaactattgctgctaagctttgtcaacatctgttgcgtgtttcttag
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G508368_T01 (Zea mays), 5'ss of exon 5
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacatcaaagaactagatgatataaagcatgatcgacctgcatttgtttagtc-taggtact-tgcttttcttg-gatgcaaacaatagtaatttgaa-----------------------------------------------------------------
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ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCTAGCAGCTCAATGGATTTCAGTTTATAATGCTAGGCGGCCCGTGAGGCAGAGgtagttacagta---tatttaattatatcatatgcta-caatgcatgatagttttgttatacgcgctgcacttctctagcaatacaaagctttgtaaacatgatcattgagatgtgatgaactattgttgctaagctttgttatcaacatccgttgcttgtttcttag
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G110085_T01 (Zea mays), 5'ss of exon 7
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattaca-----tcaaaga-actagatgatataaagcatgatcgacctgc-atttgtttagtctaggtacttgcttttcttggat--gcaaacaatagtaatttgaa-------------------------------------------------------
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ATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTTAGTTTATGATGCTAGGCGGCCCATGAAGCAGAGgtaattacaatcatttaattatattagatgctacaatgcatgatagttatgttatacgtgttgcatttct-ctagcaatacaaagctttgtaaacatgatcaatgagatgtgatgaactattgttgctaagctttgttatcaacatctgttgcttgtttcttag
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 12
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacatcaaagaactagatg-atataaagcatgatcgacctgcatttgtttagtctaggtacttgcttttcttggatgcaaacaatagtaatttgaa
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ATCTGGAAGAAGATGAGCAACCTAAGAAGAAAGTGCGATTGGGGAGTCCTGCTACTCAGTGGATATCAGTGTATAATGCTCGCCGTCCCATGAAGCAGAGgtaattaatacatcattctctgtctagcttgttcttaataatgttgcagattatttgttaaatcataaacttttcttgctttgatgcaaaagcagttgaa-
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 12
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacatcaaagaactagatgatataaagcatgatcgacctgcatttgtttagtctaggtacttgcttttcttggatgcaaacaatagtaatt-tgaa-
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ATTTGGAAGAAGATGAGCAGCCAAAGAAGAAAGTACGATTAGGTAGCCCTGCGACCCAGTGGATATCAGTTTACAATGCACGTCGTCCCATGAAGCAGAGgtaaatggat-atgttctcagtccaaatggcat-tctttaatctgtgatatatggttctgtaatatccaaactcctacatgtggtttgttttactcatggatMapped 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|218490208|gb|FG966190.1|FG966190EST: TGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAG GTACCACTATAACGTGGCTGACAACAGGCTTCAGCAGCATATAGAGAAGGG
genomic: TGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacat ... tctttgttagGTACCACTATAACGTGGCTGACAACAGGCTTCAGCAGCATATAGAGAAGGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACGCCAGGCGGGCCATGAAGCAAAGgtaattacatcaaagaactagatgatataaagcatgatcgacctgcatttgtttagtctaggtacttgcttttcttggatgcaaacaatagtaatttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG