Sequence
atgc intronic sequence ATGC exonic sequencegtttgttaagaaagagagaatgaaagcagtcttactgctaattatttgtcagtttttattcaatgcttactgaactttctattgttcagGATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTATATCCAGAGAAGTTTGAAGGTGACAAAGGGGAAAAGTTGATGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g04450.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g04450.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM5G830776_T01 (Zea mays), 3'ss of exon 14
gtttgttaagaaagagaga-atgaaagcagtcttactgctaattatttgtcagttt-ttattcaatgcttactgaactt--tctattgttcagGATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTATATCCAGAGAAGTTTGAAGGTGACAAAGGGGAAAAGTTGATGCAG
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gtttgtatagaaagagaaacaaaaaaacaggcttgctgctaagttgctgtcgttttgtttttctttgcttgacatgtttgttccattattaagGATATGAGCCCAGAAAACAAAATGAGGTTGCTGATTATATATGCAATTGTATATCCAGAGAAGTTTGAAGGTGACAAAGGGGAAAAGTTGATGCAG
upper sequence: LOC_Os06g04450.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv15s0048g00970.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------------------------------------gtttgttaagaaagaga--gaatgaaagcagtcttactgctaattatttgtcagtttttattcaatgcttactgaact--ttctattgttcagGATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTATATCCAGAGAAGTTTGAAGGTGACAAAGGGGAAAAGTTGATGCAG
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gtgatatgctaaagatttttgtctgcataggaactgatgcaccatatttctaagtaatgtccattttttatttaaaataagtttgtttggaaatgaactaa-tgcaccatattgggtaatgtctacttttttatttaaaatttgtttcacttatgcagGATGCTACTTCTGAAAATAAATTGCGTCTGTTGATGATATATGCTTCCGTTTATCCTGAGAAGTTTGAAGGTGACAAAGGTTTAAAGCTAATGCAG
upper sequence: LOC_Os06g04450.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv15s0045g00060.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------------------------------gtttgttaagaaagaga--gaatgaaagcagtcttactgctaattatttgtcagtttttattcaatgcttactgaact--ttctattgttcagGATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTATATCCAGAGAAGTTTGAAGGTGACAAAGGGGAAAAGTTGATGCAG
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gtgatatgctaaagatttttgtctgcataggaactgatgcaccatatttctaagtaatgtccattttttatttaaaataattttgtttggaaatgaactaa-tgcaccatattgggtaatgtctacttttttatttgaaatttgtttcacttatgcagGATGCTACTTCTGAAAATAAATTGCGTCTGTTGATGATATATGCTTCCGTTTATCCTGAGAAGTTTGAAGGTGACAAAGGTTTAAAGCTAACGCAGMapped 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|11025592|gb|AU162193.1|AU162193EST: TTGGAGATGCAGCAGCCAAGGAGGTGATCAGTATCCTCAGGTCAAAGCAG GATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTA
genomic: TTGGAGATGCAGCAGCCAAGGAGGTGATCAGTATCCTCAGGTCAAAGCAGgtttgttaag ... tattgttcagGATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctaattatttgtcagtttttattcaatgcttactgaactttctattgttcagGATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTATATCCAGAGAAGTTTGAAGGTGACAAAGGGGAAAAGTTGATGCAG
tgcttac putative branch site (score: 2)
ctttctatt putative PPT
aattatttgtcagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttaagaaagagagaatgaaagcagtcttactgctaattatttgtcagtttttattcaatgcttactgaactttctattgttcagGATATGAGCCCAGAAAACAAATTGAGGTTGCTTATTATATATGCAATTGTATATCCAGAGAAGTTTGAAGGTGACAAAGGGGAAAAGTTGATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG