Sequence
atgc intronic sequence ATGC exonic sequenceGTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAGgtgccattacttctttctattttgcttgcttgctctttacaacacctctgattctaatactaattctaattggtttatgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g11880.3 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G047675_T01 (Zea mays), 5'ss of exon 1
GTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAGgtgccattacttctttctattttgcttgcttgctctttacaacacctctgattctaatactaattctaattggtttatgtag
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----------CACTTTGCTCATCTCCGCCAACTTCCTATTTTGGTCCCTTATATTCCTACAGAAAATCCTCAGCTGAGTGATACTGCATATGAGgtgtggtgctaacttgtaagttccattactaat--tttaacacctatctg-ttgtaatacta-ttctgattttcttgtgtag
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G040247_T01 (Zea mays), 5'ss of exon 9
GTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAGgtgccattacttctttctattttgcttgcttgctctttacaacacctctgattctaatactaattctaattggtttatgtag
|||||||| |||||||| ||||| ||||||||| |||| || || ||||| || |||||||| |||||||||||||||||||| || || |||||| | ||| | || || || |||| || |||| || |||||||| |||| ||| || |||||
ATGGGTCTTCCACTTTGCTCATCTCCGCCAACTTCCTGTTTTGGTCCCTTATATTCCTACAGAAAATCCTCAGCTGAGTGATACTGCATATGAGgtgtggtgctaacttgtaagttccattactaat--tttaacacctatctg-ttgtaatacta-ttctgattttcttgtgtag
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G08840.1 (Glycine max), 5'ss of exon 9
GTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAGgt--gccattac----ttctttctattttgcttgcttgctctttacaacacctctgattctaatact---aattctaattggtttatgtag---------------
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ATGGGTTTTCCACTTTGCACATCTTCGTCAGCTCCCTGTTTTAGTTCCTTACATGCCTACAGAAAACCCCAGACTACGTGATACTGCTTACGAGgttagctaaaacaaagttttctctgtcacaattatgtg-tttgtgtagtatctgtaatgaactgacttgggataaaaaatcttttatgctgcttttggttctacag
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G19660.2 (Glycine max), 5'ss of exon 9
GTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAGgt--gccattac----ttctttctattttgcttgcttgctctttacaacacctctgattctaatact---aattctaattggtttatgtag---------------
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ATGGGTTTTCCACTTTGCACATCTTCGTCAACTCCCTGTTTTAGTTCCTTACATGCCTACTGAAAACCCCAGACTACGTGATACTGCTTACGAGgttagctaaaacaaagtgttctctgtcacaattaatgtgtttgcttagtatctgtaatgaactgacttgggataaaaaatattttatgctgcttttggttctacagMapped 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|58675059|gb|CK063746.1|CK063746EST: TTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAG GTTGCTCTTGTAGCTTTAACTACCAATCCTTCTTTTCATGAACTTCTCTTG
genomic: TTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAGgtgccattac ... gtttatgtagGTTGCTCTTGTAGCTTTAACTACCAATCCTTCTTTTCATGAACTTCTCTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGGGTCTTTCACTTTGCCCATCTTCGCCAACTTGCTGTATTAGTTCCTTACATACCTACAGAGAATCCTCAGCTGAGTGATACAGCTTACGAGgtgccattacttctttctattttgcttgcttgctctttacaacacctctgattctaatactaattctaattggtttatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA