Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgccgcttatctagcttaaatttcttctcaacctctgcaatcctagctgcaatgttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g38740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g38740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G032655_T01 (Zea mays), 3'ss of exon 1
gtaagcgccgcttatctagcttaaatttcttctcaacctctgcaatcctagct--gcaatgttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtg-cagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
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gtgagcttgctatagcgagctagtgtagttactagttagtaacaatcaaagtccagcagcattcggctacgctgtttggtttgcg---ctggctcctccttgacatgcatgcggatatg-------gccgtg----tggtgtggcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGCCTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
upper sequence: LOC_Os04g38740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagcgccgcttatctagcttaaatttcttc--tcaacctctgcaatcctagctgcaatgttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
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-------gtacatattcatttgcaaccggataagcgagtagtgatggagcagaatgcattggttcgtttctacattt--ttatcgaaacggctttctttcttt-ctttctttctttctttatttatttcttgtgaa----attcagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT
upper sequence: LOC_Os04g38740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagcgccgcttatctagcttaaatttcttctcaacctctgcaatcc-tagctgcaatgttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
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gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctct--cctccttgataagtgtagcttgaaa-gtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGATMapped 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|58597789|gb|CK008317.1|CK008317EST: CATCGAGCAGCACGGCCACGGCTGCTGGCGCTCGCTACCCTCCAAGGCCG GGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCC
genomic: CATCGAGCAGCACGGCCACGGCTGCTGGCGCTCGCTACCCTCCAAGGCCGgtaagcgccg ... tcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
ctctgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgccgcttatctagcttaaatttcttctcaacctctgcaatcctagctgcaatgttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG