Sequence
atgc intronic sequence ATGC exonic sequenceATGGTCTCCTGTCAAAATCGGGTGAAAGAATCCTTGTTCTTGCTGCTACAAATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttgttcggatgctccattatttcaaggaataatagatataacctgctgttgcatgatgagatgctaattcgtttcccttatttggttgaacag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50750.2 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G128748_T01 (Zea mays), 5'ss of exon 12
ATGGTCTCCTGTCAAAATCGGGTGAAAGAATCCTTGTTCTTGCTGCTACAAATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttgttcggatgctccattatttcaaggaataatagatataac-ctgctgttgca-tgatgagatgctaattcgtttcccttatttggttgaacag
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ACGGTCTCTTGTCAAAAACAGGCGAAAAAATCCTCGTTCTCGCCGCGACGAATAGGCCTTTCGACCTTGATGAAGCCATCATCAGGAGATTCGAGCGCAGgtccgtttccatac-ctaccgtaccttt--ttttctgatgcaacgcaagtccagcgctgatcgtttgc--gcttgcgcttgtcggtttactgaacag
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA01G43230.1 (Glycine max), 5'ss of exon 12
ATGGTCTCCTGTCAAAATCGGGTGAAAGAATCCTTGTTCTTGCTGCTACAAATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttg---ttcggatgctccattatttcaaggaataatagatataacctgctgttg-catgatgagatgctaattcgtttcccttatttg-gttgaacag---------------------------------------------------------------------
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ATGGACTTATGACAAATTCGGGGGAGCGCATCCTTGTTCTTGCTGCAACCAATAGGCCATTTGACCTCGATGAAGCAATAATTAGGAGATTTGAAAGGAGgtatggtatctctatgtttatgttttcctctttgatgtaaatttaaatcgagggaggtaaaagcagatatgaaggctatatatatgttcgtgacaatctgaattccatgaaattcagtaataatatttgatcatttgtgcttactataatgctcatcttttgtttacag
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA11G02270.1 (Glycine max), 5'ss of exon 8
ATGGTCTCCTGTCAAAATCGGGTGAAAGAATCCTTGTTCTTGCTGCTACAAATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttgttcggatgctccattatttcaaggaataata-------------gatataacctgctgttgcatgatg-agatgctaattcgtttccctta-tttggttgaacag---------------------------------------------------------------
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ATGGACTTATGACAAACTCCGGGGAGCGCATCCTTGTTCTTGCTGCAACCAATAGGCCATTTGACCTCGATGAAGCAATAATTAGGAGATTTGAAAGGAGgttgccacaatatttctactttcttcatctatgtttatgtttcctctttgatgtaaatttaaatcgagggagggagaagctgatatgtttgttacaatctgaatgccctgaaattcagtaataatatttgatcatttgtgcttatttctacaatgctcgtcttttgtttacag
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G52882.1 (Arabidopsis thaliana), 5'ss of exon 9
ATGGTCTCCTGTCAAAATCGGGTGAAAGAATCCTTGTTCTTGCTGCTACAAATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttgttcggatgctccattatttcaaggaataatagatataacctgctgttgcatgatgagatgctaattcgtttcccttatttggttgaacag
|||| || || | ||| | |||||||| || || |||||||| || ||||| ||||| ||||||||||||||||| ||||||||||| |||||| | |||| | | | | | | || | | || || || | | || || || || ||| | | | || | | |||||
ATGGGCTAATGACGAAACCCGGTGAAAGGATTCTCGTTCTTGCAGCGACAAACAGACCGTTTGATCTTGATGAAGCTATCATTAGGAGGTTTGAGAGAAGgtataaaagaaattttggtaa----aatgcaaaacctcta-aatcagtctttacactattttg-actgatttttgttttgtgttggatataacag
upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 5'ss of exon 13
ATGGTCTCCTGTCAAAATCGGGTGAAAGAATCCTTGTTCTTGCTGCTACAAATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttgttcggatgctccattatttcaaggaata-----atagatataacctgctgttgcatgatgagatgctaattcgtttcccttatttggttgaacag-
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ATGGGCTACTGACAAAAGCTGGTGAACGAATCCTTGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAGgtagatttgtatattgtattacactcagcatcattctcatcgttttactgcatcccttaatcttcaactacaaaaaaggc-cagatcttcatcaaagcatgMapped 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|24468881|gb|CA305830.1|CA305830EST: AATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAG AATCATGGTTGGCCTTCCAACTCTAGATAGCAGAGAGCTGATCTTAAGGAC
genomic: AATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttgttcgg ... ggttgaacagAATCATGGTTGGCCTTCCAACTCTAGATAGCAGAGAGCTGATCTTAAGGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGGTCTCCTGTCAAAATCGGGTGAAAGAATCCTTGTTCTTGCTGCTACAAATAGACCCTTTGATCTTGATGAAGCCATCATTAGGAGATTTGAGCGCAGgtttgttcggatgctccattatttcaaggaataatagatataacctgctgttgcatgatgagatgctaattcgtttcccttatttggttgaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT