Sequence
atgc intronic sequence ATGC exonic sequenceACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 7
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaatc-at-ctgcatttcttttc-cattttaatttcg---tatattgataaatttagaacttcctcatccttttttattgtactgcatattag
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ATATGGCTGAGAGGCAGTGGGCTGAGGCTGCGACTGATTTCTTTGAAGCTTTCAAGAACTACGATGAAGCAGGCAATCCACGGAGAATCCAATGCCTAAAgtatactcatctatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattag
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 7
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaa-tcatctgcatttc-----ttttccattt----------taatttcgtatattgataaatt-tagaacttcctcatcctt----ttttattgtactgcatattag
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ATATGGCTGAGAGGCAGTGGGATGAGGCTGCCACTGATTTCTTTGAAGCTTTCAAGAACTATGATGAAGCAGGCAATCCGCGGAGAATTCAATGCCTAAAgtacttatacttatttaaacttcaacagttcttcacttcttcctgatcttagttcataggtacataaattctagaacactgtgatacatatcatttttttttgctgtgcattag
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G17660.1 (Glycine max), 5'ss of exon 7
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattag-----------------
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ATATGGCTGAGCGCCAGTGGGCAGATGCAGCTACTGATTTCTTTGATGCTTTCAAGAATTATGATGAAGCTGGTAGTCAGAGACGTATCCAATGTTTGAAgtaggtgaagca---gcattctttttac----tatctgtatatagcaataactttata--tttcacttcagcatataaaacaatgta-attaaccacaataactattttg
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 7
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaatcatctgcatttcttttccatttt--aatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattag------
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ATATGGCAGAGCGCCAGTGGGCAGAAGCAGCTACTGATTTCTTTGAAGCTTTCAAGAATTATGATGAAGCTGGGAGTCAGAGACGTATCCAATGCTTGAAgtaggtgaagtagcattcttttactatcagtttcaaacaatgtatatagaaataactttatatttcacttcagcatataaaacaattta-attaaccacag
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 7
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgta----------------atcaaatcatctgcatttcttttccattttaatttcgtat-attgataaa------tttagaact-tcctcatccttttttattgtactgcatattag-----------------
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ATATGGCAGAGCGCCAATGGGCAGATGCAGCAACTGACTTTTTTGAAGCTTTTAAGAATTATGATGAAGCTGGGAATCAGCGACGTATCCAATGCTTAAAgtatgctatggcttgggaagttgaattatttactcgtcttttatatgtctattttgaaagattcataagcatatttttataatcattttggtactattgtttgacactggatctatttctgcaccacctgatag
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 7
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaatcatctgc-atttcttttccattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgca-tattag-----
||||||||||| |||| ||||| | ||| || ||||| || ||||| |||||||| ||||| ||||| ||||| | | ||||||| || || ||||||| ||| || || | || ||| || | | | | | | | | ||| | | || | || |
ACATGGCTGAGCGGCAGTGGGCCGTTGCAGCCACTGACTTTTTTGATGCATTCAAGAACTACGATGAGGCTGGTACCCACAGGAGAATCCAGTGTTTGAAgtatgtgaatttcaaattgcttgttcttcaagttacttgcttcgagctgtgagtcggtagtaattggaagttttagaaataatttgaagtaactgaagta
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 7
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaatcatctgcattt-----cttttccattttaatttcgtatattgataaatttagaacttcct----catccttttttattgtactgcatattag---------------------------
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ATATGGCTGAGCGACAGTGGGCAGTTGCCGCCACCGACTTTTTTGATGCATTCAAAAACTACGATGAGGCTGGCACCCACAGGAGGATCCAATGTCTGAAgtgagtttgtttggtacgcttaaagtttcttgtatcatgagtttgtttggagtttcagtaacaacttcctgaagcatactcttctgagtgacgagaactttgttaacaaggttttggatgggattgcagMapped 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|55827482|gb|AU032236.2|AU032236EST: TTCAAAAACTATGATGAAGCTTGCAATCCGCGGGGAATTCAATGCCTGAA ATATCTTGTTCTTGCAA-TATGTTG
genomic: TTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaat ... tgcatattagATATCTTGTTCTTGCAAATATGTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACATGGCTGAGAGGCAATGGGCAGATGCTGCAACTGATTTCTTTGAAGCATTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA