Sequence
atgc intronic sequence ATGC exonic sequenceTGGTCTCTTACCCGAGGAACATGTGACGCTGTGTTAGCATGCCATGCTGGCCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgaccattgcttattttaaaactggggagatgagctctatcacatatccactgtactctacagtattcatcatcaaataatgctcttcatgtcaaatgagtctgatccttaattaacatcccag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39380.3 |
intron # | 29 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM2G074466_T01 (Zea mays), 5'ss of exon 9
TGGTCTCTTACCCGAGGAACATGTGACGCTGTGTTAGCATGCCATGCTGGCCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgaccattgcttattttaaaactggggagatgagctctatcacatatccactgtactctacagtattcatcatcaaataatgctcttcatgtcaaatgagtctgatccttaattaacatcccag
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TGGTCCCTTAACCGGGGAACATGTGATGCAGTGTTAGCATGCCATGCTGGTCCCGTACTATGTGTGGAATACTCACCTTCAGATAAAGGAATTATCACTGgtatgtgactatatctcattttaagaacagggtggc-------------------ctgaattgt---ggatctatagttgaata---ttctgcatgct-------tctgattcttaatt--tattccag
upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GLYMA08G04510.1 (Glycine max), 5'ss of exon 28
TGGTCTCTTACCCGAGGAACATGTGACGCTGTGTTAGCATGCCATGCTGGCCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgaccattgcttattttaaaactggggagatgagctctatcacatatcca----ctgtactctacagtattcatcatcaaataatgctcttcatgtcaaatg---agtctgatccttaattaacatcccag
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TGGTCTGTTTCCCGAGGAACAATGGATGCTGTCTTAGCTTGCCATGCTGGGCCAATATTATGTGTTGAGTATTCTTCTTTAGACAGAGGAATAATTACAGgtgcgtcatctccaattttttgctatgctgccatttggtatcttttattttgttggttcttgggcttgcttgaagagaaatttccactgtgctttt-atatccagtgcttactaaaatgttaaatttccattctag
upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GLYMA05G35210.1 (Glycine max), 5'ss of exon 12
TGGTCTCTTACCCGAGGAACATGTGACGCTGTGTTAGCATGCCATGCTGGCCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgaccattgcttattttaaaactggggagatgagctctatcacatatcca----ctgtactctacagtattcatcatcaaataatgctcttcatgtcaaatg---agtctgatccttaattaacatcccag
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TGGTCTGTTTCTCGAGGAACATGTGATACTGTCTTAGCATGCCATGCTGGACCAATATTATGTGTTGAGTATTCTTCTTTAGATAGAGGAATAATTACAGgtgcttcatctccaattttttgctatgctgccatttgatatcttttattttgttggttcttggacttgcttgaagagaaatttccgccatgctttttatatccagtgcttactaaaatgttaaatttccattccagMapped 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|66923642|gb|CX110490.1|CX110490EST: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAA
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGTCTCTTACCCGAGGAACATGTGACGCTGTGTTAGCATGCCATGCTGGCCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgaccattgcttattttaaaactggggagatgagctctatcacatatccactgtactctacagtattcatcatcaaataatgctcttcatgtcaaatgagtctgatccttaattaacatcccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA