Sequence
atgc intronic sequence ATGC exonic sequenceATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgtggattaggaacttactatatctagcttatctggtttatacttatttagttgacatgggtcagtaatgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g36960.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G137118_T02 (Zea mays), 5'ss of exon 4
ATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgttt-gtggattaggaacttactat-atctagcttatctggtttatacttatttagttgacatgggtcagtaatgcag
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ATGGCTCTAATTGCTCGGCTGCAGCACCCTTACATTGTTGAATTCAAGGAGGCTTGGGTTGAGAAGgttttgtagttcaggaacttgttcttaccttgtttcttctgtttgaacttatttagttgaca-aggtgagttatgcag
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G31330.1 (Glycine max), 5'ss of exon 3
ATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgtggattaggaac-------ttactatatctagcttatctggtttatacttatt-tagttgacatgggtcagtaatgcag---------------------------------------------
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ATGGCTCTTATTGCTCGAATTCAGCATCCCTACATTGTGCAATTTAAAGAGGCTTGGGTTGAGAAGgttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtag
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G18340.1 (Glycine max), 5'ss of exon 3
ATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgtggattaggaacttactatatctagcttatctggttt--atacttatttagttgacatgggtcagtaatgcag------------------------------------
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ATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAGgtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagt-attgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcag
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G09910.1 (Glycine max), 5'ss of exon 3
ATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgtggattaggaacttac-tatatctagcttat---ctggtttatacttatttagttgacatgggt--cagtaatgcag------------------------------------------------------------------------
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ATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAGgtgaagacccttaaaatttttgtataatgtaatcatagacttagtttctttcagttaattgttaatagttacagtattgcaatctctgttgtgaactagaagtgtgagaataatgactgtttacttttctgctaagcacattctactgttgcag
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G38980.1 (Glycine max), 5'ss of exon 3
ATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgt----ggattaggaacttactat-atctagct-tatctggt-ttatac-ttatttagttgacatgggtcagtaatgcag--------------------------------------------------
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ATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAGgtgagccaaagcattgcgtttcgattgttattttgcagtatgcagtgttgtacgttctcctgtaaacttgaattagttgtattgtaatggttttatttatttattacttaagtatgtttttggttgtattgtag
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 5'ss of exon 3
ATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgt---ttgtgga----ttaggaacttactatatctagcttatctgg-------tttatacttatttagttgacatgggtcagtaatgcag
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ATGGCTCTAATTGCGAGAATCCAACACCCTTACATTGTTGAATTTAAGGAAGCATGGGTAGAGAAGgtaggtcctggaaattctagttttttgacgaatttttttgctgtaaatgcgaccttgtactgaatcgagagctttgggttgg-aatgcagMapped 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|88402749|gb|CI613197.1|CI613197EST: GGTTGCCACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAG GGTTGCTATGTCTGCATTGTCACG
genomic: GGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgtggat ... agtaatgcagGGTTGCTATGTCTGCATTGTCACG
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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAGgtttgtggattaggaacttactatatctagcttatctggtttatacttatttagttgacatgggtcagtaatgcag
- - - - - - - - - - - - - - - - - - - - - - - AAGAGG