Sequence
atgc intronic sequence ATGC exonic sequenceAAGTGTCAACGAGTCATGGGACAATGCTAATGAAGGCACTGGAAGCCATGTTCCTTCTTCTTCTGGTTCTCCTAAGAAGTTGGATGGACATTGTAAAGAGgtacacatttttattccttacattgtcatgtgactgttagtggagagagaattactaatacaggaagtactgccgacctgcaatcttatttttctgctttatcatgtgcttttttggggggattag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g39870.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G048553_T02 (Zea mays), 5'ss of exon 5
AAGTGTCAACGAGTCATGGGACAATGCTAATGAAGGCACTGGAAGCCATGTTCCTTCTTCTTCTGGTTCTCCTAAGAAGTTGGATGGACATTGTAAAGAGgtacacatttttattccttacattgtcatgtgactgttagtggagagagaattactaatacaggaagtactgccgacctgcaatcttatttttctgctttatcatgtgcttttttggggggattag
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AAATGCCGATGAATCATATGCAAATGCTGCTGAAGGCAGTAGCAGACATGTTCTTTCTTCGTCTGGTTCTCCGAAGAAGTCGGATGGTCATTGTAAAGAGgtactaagtgctacttgtaccatggctgtgttgtttcgtctt------tcttttctgat-taatcttctttgcaaggttagtgtcctattttga-attttatttattactttct---gggggctag
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G017334_T01 (Zea mays), 5'ss of exon 5
AAGTGTCAACGAGTCATGGGACAATGCTAATGAAGGCACTGGAAGCCATGTTCCTTCTTCTTCTGGTTCTCCTAAGAAGTTGGATGGACATTGTAAAGAGgtacacatttttattccttacattgtcatgtgactgttagtggagagagaattactaatacaggaagtactgccgacctgcaatcttatttttctgctttatcatgtgcttttttggggggattag
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AAATGCTGATGAATCATGGGTAAATGCTGCTGAAGGTAGTAGCAGTCATGTTCAATCATCATCCGGTTCTACGAAGAAGTTGGATGGACATTGTAAAGAGgtactaactgctacttgtaccat------------------------ggaattaatcatctttgtaaggctagtgtcct---attttgaatttt--ctttatta----cttttttggggctag---Mapped 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|86496967|gb|CI139600.1|CI139600EST: TTCCTTCTTCTTCTGGTTCTCCTAAGAAGTTGGATGGACATTGTAAAGAG ATTAAAGAATCAGCAGCGGCATCTGGAAGTGATGATGACG
genomic: TTCCTTCTTCTTCTGGTTCTCCTAAGAAGTTGGATGGACATTGTAAAGAGgtacacattt ... gggggattagATTAAAGAATCAGCAGCGGCATCTGGAAGTGATGATGACG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGTGTCAACGAGTCATGGGACAATGCTAATGAAGGCACTGGAAGCCATGTTCCTTCTTCTTCTGGTTCTCCTAAGAAGTTGGATGGACATTGTAAAGAGgtacacatttttattccttacattgtcatgtgactgttagtggagagagaattactaatacaggaagtactgccgacctgcaatcttatttttctgctttatcatgtgcttttttggggggattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA