Sequence
atgc intronic sequence ATGC exonic sequence...ttggatacatgcagacctatcaataattcaatgtgcttatttttctccgtgtgtcatattggttgtttttgaacaatctcataattctctctgcatacagCTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATCAGAGATGCTCTTGAAGTTTCTGCTGAAATGTATAAGAAGGACCCAAACA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39380.3 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G074572_T01 (Zea mays), 3'ss of exon 17
ttggatacatgcagacctatcaataattcaatgtgcttat-ttttctccgtgtgtcatattggttgtttttgaacaatctcata--attctctctgcatacagCTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATCAGAGATGCTCTTGAAGTTTCTGCTGAAATGTATAAGAAGGACCCAAACA
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---atcacatctatattttaccaggttatgaaactcacatgttctatatgcttgcagagctaagcaatctgaaacaacctcattgcatttttttcacgtgcagCTTAAGATGGCTATAACTCTTGCGAACTCTCGCAACGACCTGGCGACCATTAGAGATGCTCTTGAAGTTTCTGCTGAAATGTACAGAAAAGACCCAAACA
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA08G04510.1 (Glycine max), 3'ss of exon 17
ttggatacatgcagaccta-tcaataattcaatgtgcttatttttctccgtgtgt-catattggttgtttttgaacaatctcataattctctctgcatacagCTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATCAGAGATGCTCTTGAAGTTTCTGCTGAAATGTATAAGAAGGACCCAAACA
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--gataacttattcccttaatttctaattgagtaaattcttttttttagaaaaatatttcttaattttcttcttgtctctttttgaatttgtttattttcagCTTAAAACAGCTATTAATCGCGCAACATCACGTAATGACTTGTTGACCATTAGAGATGCTCTTGAAGTTTCTTCTGATATGTATAAGAAAGATAATAATA
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 17
-----ttggatacatgcagacctatcaataatt-caatgtgcttatttttctccgtgtgtcatattggttgtttttgaacaatctcataattctctctgcatacagCTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATCAGAGATGCTCTTGAAGTTTCTGCTGAAATGTATAAGAAGGACCCAAACA
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atttgtttgtttctaataaaaataataataataataatat-cttatttcattttgtaggacgatctaatttttttt---tcttctttcaaatgtgccac--ttcagCTCAAAACTGCAATTGGTCGTGCAACCTCTCGGAATGACATGCCCACCATCAGAGATGCACTTGAGGTGTCTGCTGAAATGTATAAGAAAGACGCTAATAMapped 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|163926735|gb|EG713751.1|EG713751EST: GTTGGCAATGCCGATTAACTGATGAACAGTTTATTGCTGTAAAAGAACTG CTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATC
genomic: GTTGGCAATGCCGATTAACTGATGAACAGTTTATTGCTGTAAAAGAACTGgtgagatgaa ... ctgcatacagCTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccgtgtgtcatattggttgtttttgaacaatctcataattctctctgcatacagCTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATCAGAGATGCTCTTGAAGTTTCTGCTGAAATGTATAAGAAGGACCCAAACA
ttctctctgc CT-rich tract
ttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggatacatgcagacctatcaataattcaatgtgcttatttttctccgtgtgtcatattggttgtttttgaacaatctcataattctctctgcatacagCTCAAGACGGCTATAACTCGTGCCAACTCCCGCAATGACATGCTAACCATCAGAGATGCTCTTGAAGTTTCTGCTGAAATGTATAAGAAGGACCCAAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG