Sequence
atgc intronic sequence ATGC exonic sequenceACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAGgtatggttgttttcatcactgaggcagtgtctcaatgttttttttattatctctgttcaaatattggactttgtggtctcagtttcccctttcctctctttgactctttgttag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52690.3 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G058141_T02 (Zea mays), 5'ss of exon 2
ACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAGgtatggttgttttcatcactgaggcagtgtctcaatgttttttttattatctctgttcaaatattggactt-tgtggtctcagtttcccctttcctctctttgactctttgttag
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ACGCCCATGTGTCATTTTCTTTGATGAGCTTGATTCCCTCGCTCCTGCACGAGGATCCTCAGCAGATTCTGGCGGTGTCATGGACAGGGTTGTTTCCCAGgtatcattagcttcgtccctgaggcggtgtcacaac--ttctcacaagtcttctgttaaattactgggccagtgtcttctcacttcccccccttttcgtgtctactag-------
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G445617_T01 (Zea mays), 5'ss of exon 11
ACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAGgtatggttgttttcatcactgaggcagtgtctcaatgttttttttattatctctgttcaaatattggactttgtggtctcagtttcccctttcctctctttgactctttgttag
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ACGCCCATGTGTCATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCAGCAGATTCTGGCGGTGTCATGGACAGGGTTGTTTCCCAGgtatcattagcttcgtccctgaggcggtgtcacaac--ttctcacaagtcttctgttaaattactgggc----cagtgtc---ttctcacttccccccttttcgtgtctactag
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA19G39580.1 (Glycine max), 5'ss of exon 11
ACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAGgtatggttgttttcatcactgaggcagtgtctcaatgttttttttattatctctgt-tcaaatattggactttgtggtctcagtttcccctttcctctctttgactctttgttag
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ACGTCCATGTGTCATCTTCTTTGATGAGCTTGATTCTCTTGCACCAGCTCGAGGTGCCTCTGGAGATTCTGGGGGTGTTATGGACAGAGTGGTTTCTCAGgtg-----atttcctactccgag-caagaccatgatgtttgcagttttttctctgggtttcctaacgtaatatattccccttgttatag--------------------------
upper sequence: LOC_Os04g52690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 5'ss of exon 11
ACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAGgtatggttgttttcatcactgaggcagtgtctcaatgttttttttattatctctgttcaaatattggactttgtggtctcagtttcccctttcctctctttgactctttgttag
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ACGTCCATGTGTTATCTTCTTTGATGAACTTGATTCTCTTGCTCCAGCCCGAGGTGCCTCTGGGGATTCTGGGGGTGTTATGGACAGAGTAGTTTCCCAGgtgaagacatttttgtgatggttaatgcggattg-tgtttttctt-ttatttccct---aatggtg-acctcattgtgggaaatccccttgctaccag----------------Mapped 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|29675898|gb|CB672173.1|CB672173EST: GAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAG TTGCTTGTGGAGATTGATGGGTTAAGCGATAACAGTCAG
genomic: GAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAGgtatggttgt ... tctttgttagTTGCTTGTGGAGATTGATGGGTTAAGCGATAACAGTCAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACGGCCATGTGTAATTTTCTTTGATGAGCTTGATTCCCTTGCTCCTGCACGAGGATCCTCCTCAGATTCCGCAGGTGTGATGGATAGAGTAGTTTCACAGgtatggttgttttcatcactgaggcagtgtctcaatgttttttttattatctctgttcaaatattggactttgtggtctcagtttcccctttcctctctttgactctttgttag
- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA