Sequence
atgc intronic sequence ATGC exonic sequenceTGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagtttttttgatagtattttaactgttcatcattcactaaggatgaagtacattcaactctgggtgtctttgttcctgagtaaaaacttaaatgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g43630.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AC198725.4_FGT007 (Zea mays), 5'ss of exon 8
TGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagtttttttgatagtattttaactgttcatcattcactaaggatgaagtacattcaactctgggtgtctttgttcctgagtaaaaacttaaatgtag
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TGGAAAAATAGCACTGCAGCAGTATGATGTTAATGCTATTGTGGACAGGCTTCTACAATTTCTTGAAATGGATAAGGATTATGTGACTGCTGAAACTCTAgtaagtgtttgtaatgctagtt--actgacc----tttactcatgatctattctaacaggattctgatttacacatgcag--------------------
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G029077_T01 (Zea mays), 5'ss of exon 6
TGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagtttttttgatagtattt-----taactgttcatcattca--cta--aggatgaag---tacattcaactctgggtgtctttgttcctgagtaaaaacttaaatgtag
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TGGAAAAATAGCACTGCAGCAGTATGATGTTAATGCCATTGTGGACAGGCTTCTACAATTTCTTGAAATGGATAAGGATTATGTGACTGCTGAAACTCTAgtaagtgtttgtaatgctagttactgatctttactcatgatctagtctagcaggattacgatttacattccact-tgtatcttgatgttttggatttaaaaataaaacgcag
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA06G08590.1 (Glycine max), 5'ss of exon 6
TGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagtttttttgatagtattttaactgttc----atcattcactaaggatgaagtacattcaactctgggtgtctttgttcctgagtaaaaacttaaatgtag------------------------------------------------------------
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TGGGAAGATAGCATTGCAGCAGTATGATGTCAATGCTATTGTTGATCGACTTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTGgtaaacatgacaagt-gcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgcaaacatgtgttgaaagtaaggcattttgatttgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcag
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA04G08480.1 (Glycine max), 5'ss of exon 6
TGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagtttttttgatagtattttaactgttc----atcattcactaaggatgaagtacattcaactctgggtgtctttgttcctgagtaaaaacttaaatgtag------------------------------------------------------------
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TGGGAAGATAGCATTGCAGCAGTATGATGTCAATGCTATTGTTGATCGACTTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTGgtaaacatgacaagt-gcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgcaaacatgtgttgaaagtaaggcattttgatttgacttagctatggtatggtagactaatgcgaagtttgaaagttcatttgttcag
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G11490.2 (Arabidopsis thaliana), 5'ss of exon 6
TGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagttttt-ttgatagtattt-------taactgttcatcattcactaaggatgaagtacattcaactctgggtgtctttgttcctgagtaaaaacttaaatgtag
||| || || || |||| ||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| ||||| |||||||| ||||||||| | |||| | | || | |||| | | || ||||| || | | | | | || | | | || | || | || | |||
TGGAAAGATTGCTTTGCAACAGTATGATGTAAATGCGATTGTTGATAGACTTCTTCAATTTCTGGAGATGGAAAAGGACTATGTGACCGCTGAAACTTTGgtaaactatcatttgaactattcacggagatgattggccatca--cattgatacttatattgtttacattttcataacaattccacttgtctggttcctct--tctag
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv04s0008g03880.t01 (Vitis vinifera), 5'ss of exon 6
TGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagtttttttgatagtattttaactgttcatcattcactaaggatgaagt---acattcaac-----tctgggtgtctttgt-----tcctgagtaaaa---acttaaatgtag----------------------------------------------------
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TGGGAAAATAGCACTGCAGCAGTATGATGTGAATGCTATCGTTGATAGGCTTCTTCAATTTCTTGAGATGGAGAAGGACTATGTGACTGCTGAAACTCTGgtgaatttttacagctgtgcctagatgcttggatttttattgtgattgaatttgaacattgaaccaaactccaaaaaaatttatgctcttcatgcatagaagtaacatgagcatatgatttaactgttattaatcagattgatacaagtctggagttctctcatgtagMapped 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|66915427|gb|CX102275.1|CX102275EST: TTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTT GTCTTGGTGAAAGATCTTTTGAGGAAATATCCTCAATGGAGCCATGATTGT
genomic: TTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagttttt ... ttaaatgtagGTCTTGGTGAAAGATCTTTTGAGGAAATATCCTCAATGGAGCCATGATTGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGGAAAATAGCGCTGCAGCAGTATGATGTGAATGCTATTGTTGACAGGCTTCTGCAATTCCTTGAAATGGACAAGGAATATGTGACGGCTGAAACTCTTgtaagtttttttgatagtattttaactgttcatcattcactaaggatgaagtacattcaactctgggtgtctttgttcctgagtaaaaacttaaatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA