Sequence
atgc intronic sequence ATGC exonic sequence...ggtggaaaaggtcgtcatttcaggatgtagatatataagttagggcatatcctcttactttatatggtggttcattaacatgtactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCGACATGGAAACTAGGGCACCAAGGCCTCTATGCCCTCATTTCCACCTTGCAGCGAGCAAACTGCGAAGATCCTCTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37410.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37410.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G131756_T01 (Zea mays), 3'ss of exon 16
------ggtggaaaaggtcgtcatttcaggatgtagatatataagttagggcatatcctcttactttatatggtggttcattaacatgtactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCGACATGGAAACTAGGGCACCAAGGCCTCTATGCCCTCATTTCCACCTTGCAGCGAGCAAACTGCGAAGATCCTCTAA-----
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atttcagacacacaaag--gtcatgaacggaagcag-tctctaggtttcaac-tccacaatgaatttctgaacgaaacaagtaaactgtggctg--tcttacgcagGATTTGTCTGTGTGCGAGGATTCGACATGGAGACTAGAGCACCAAGGCCTCTGTGCCCCCATTTGCACATTATAGCAAGGC-----CGAAGGCCCGCAAGACAGC
upper sequence: LOC_Os05g37410.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G141792_T01 (Zea mays), 3'ss of exon 2
------ggtggaaaaggtcgtcatttcaggatgtagatatataagttagggcatatcctcttactttatatggtggttcattaacatgtactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCGACATGGAAACTAGGGCACCAAGGCCTCTATGCCCTCATTTCCACCTTGCAGCGAGCAAACTGCGAAGATCCTCTAA-----
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atttcagacacacaaag--gtcatgaacggaagcag-tctctaggtttcaac-tccacaatgaatttctgaacgaaacaagtaaactgtggcta--ttttacgcagGATTTGTCTGTGTGCGAGGATTCGACATGGAGACTAGAGCACTCAGGCCTCTGTGCCTCCCATTAGCACATATAGCAAGGC-----CGAAGGCCCGCAAGACAGC
upper sequence: LOC_Os05g37410.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G020977_T01 (Zea mays), 3'ss of exon 3
ggtggaaaaggtcgtcatttcaggatgtaga-tatataagttagggcatatcctcttactttatatggtggttcattaacatgtactaaaa---tgcaatgcagGATTTGTCTGTGTGAGAGGATTCGACATGGAAACTAGGGCACCAAGGCCTCTATGCCCTCATTTCCACCTTGCAGCGAGC---AAACTGCGAAGATCCTCTAA
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-acacacaaag--gtcatgaacggaagcagtctctactctctagccttcaactccacaatgaatttc-tgaacgaaacaagtaaactgtggctgtcttacgcagGAGTTGTCTGTGTGCGAGGATTCGACAGGGAGACTAGGGCACCAAGGCCTCTGTGCCCCCATTTGCACATTGTAGCAAGGCCGAAAGTCCGCAAGACAGC---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|58677144|gb|CK065831.1|CK065831EST: GTCTAACAACTGAAGAAATACAGCACTGCTTCTGGAGAG GATTTGTCTGTGTGAGAGGATTCAACATGGAAACTAGGGCACCAANGCCTC
genomic: GTCTAACAACAGAAGAAATACAGCACTGCTTCTGGAGAGgtattaacag ... tgcaatgcagGATTTGTCTGTGTGAGAGGATTCGACATGGAAACTAGGGCACCAAGGCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatcctcttactttatatggtggttcattaacatgtactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCGACATGGAAACTAGGGCACCAAGGCCTCTATGCCCTCATTTCCACCTTGCAGCGAGCAAACTGCGAAGATCCTCTAA
tactaaa putative branch site (score: 1)
ttactttatat TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtggaaaaggtcgtcatttcaggatgtagatatataagttagggcatatcctcttactttatatggtggttcattaacatgtactaaaatgcaatgcagGATTTGTCTGTGTGAGAGGATTCGACATGGAAACTAGGGCACCAAGGCCTCTATGCCCTCATTTCCACCTTGCAGCGAGCAAACTGCGAAGATCCTCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtac