Sequence
atgc intronic sequence ATGC exonic sequence...tgtttttttattggtcttgaatatcttatatttggtggaatgaatctatattccagcttactacgtttcaagaatggctactgatgtttcctttatatagGGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATCAGAAAGGTGGTTGCCAGAACTGAGAAACGCAGTTCAAGAGGCTCAAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g21780.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 8
tgtttttttattggtcttgaatatcttatatttggtggaatgaatctatattccagcttac-----tacgtttcaagaatggctactgatgtttc----ctttatatagGGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATCAGAAAGGTGGTTGCCAGAACTGAGAAACGCAGTTCAAGAGGCTCAAAGG
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--------caatg-caaaggagatattatctacagtgggaatatttgttctatctggttaaatggatgtgttttcaggacacatactgatatgtcatgtctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGTGGTGAGTGAAAGATGGCTTCCGGAACTGAGAAATGCAGTTCAAGAAGCTCGAAGG
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G055917_T01 (Zea mays), 3'ss of exon 8
--------------------------------------------------------------------------------------tgtttttttattggtcttgaatatcttatatttggtggaatgaatctatatt-ccagcttactacgtttcaagaatggctactgatgt----ttcctttatatagGGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATCAGAAAGGTGGTTGCCAGAACTGAGAAACGCAGTTCAAGAGGCTCAAAGG
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gtacattgcgttttatttattttttaggtcaattgcagtagttatactgaatctggccagaaactgcttcaacacgaaagagatattgtctacatttttttactctgtttatttcagttggaatatttgttctatctggtcaaatgaatgtgttttcagaacacgtactgatatggcatgtctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAGTGAAAGATGGCTTCCGGAGCTGAGAAATGCAGTTCAAGAAGCTCGGAGGMapped 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|88340089|gb|CI650536.1|CI650536EST: GATCGTGTTTTGCTGAACCGAGCACATCGTGCTCAACAGGAATATGAAAG GGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATC
genomic: GATCGTGTTTTGCTGAACCGAGCACATCGTGCTCAACAGGAATATGAAAGgtacgctgaa ... ctttatatagGGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatattccagcttactacgtttcaagaatggctactgatgtttcctttatatagGGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATCAGAAAGGTGGTTGCCAGAACTGAGAAACGCAGTTCAAGAGGCTCAAAGG
tactgat putative branch site (score: 2)
tgtttccttt CT-rich tract
tttatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttttttattggtcttgaatatcttatatttggtggaatgaatctatattccagcttactacgtttcaagaatggctactgatgtttcctttatatagGGTGGCCAACTACTGTCTTAAATTAGCTGGTGAACAAGAAAAGATGGTATCAGAAAGGTGGTTGCCAGAACTGAGAAACGCAGTTCAAGAGGCTCAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG