Sequence
atgc intronic sequence ATGC exonic sequencegtagagcttctgttttgttgtcatcatttttttctttcttgttgccctttgccttcatccctgtagatttgcactgctgatcttactagttttgcagCTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCCATAATGATATTGGCAATGAGATACCTGTCCACCTGCAAAGAACACAGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g38590.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G011078_T02 (Zea mays), 3'ss of exon 5
--------gtagagcttctgttttgttgtcatcatttttttctttcttgt-tgccctttgccttcatccctgtagat----ttgcactgctgatcttactagttttgcagCTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCCATAATGATATTGGCAATGAGATACCTGTCCACCTGCAAAGAACACAGTA
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gtggagtctcagagttcatcgtctgacgtcgcttcgctattgttttttgggcatcatttcctcacatcgataataacatcatcgtcatcgtcatccatgttctcttgcagCTGGTATCGTGTTGGAAGAGAAGAACTGGCCCCCGTTTTTCCCCATCATTCATAACGATATCGGCAACGAGATACCTGTCCATCTGCAAAGAACGCTGTA
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 5
gtagagcttctg--ttttgttgtc----atcatttttttctttcttgttgccctttgc-----cttcatccctgtag----------atttgcactgctgatcttactagttttgcagCTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCCATAATGATATTGGCAATGAGATACCTGTCCACCTGCAAAGAACACAGTA
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gtggagtttcagagtgtcatcatccgacgtcgctttgctatcttttggcgtcattcacgaggactccctttcgttaatgataataatacgagcatcgtt-atccatctcctcttgcagCTGGCGTTGTGTTGGAAGAGAAAAACTGGCCACCGTTTTTCCCCATCATCCATAACGATATTGGCAACGAGATACCTGTCCATCTGCAAAGTACACTGTA
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S297_59V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------------------gtagagcttctgttt-----tgttgtcatcatttttttctttcttgttgccc--tttgccttcatccctgtagatttgcact--gctgatcttactag---ttttgcagCTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCCATAATGATATTGGCAATGAGATACCTGTCCACCTGCAAAGAACACAGTA
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gtgagtgtagttttgttcatactcctctgaatctctaagtgcattggaattgttgacagttaatctggagttagctgaaatcatgtcgattgttgcaattatgtttggagttggggtcaggaggtaggttttacctatgtccaaatcaaatttagtgtgcgttgtcgcgtgattcgttgactttggttggcatttttcagCTGGCATACTTATTGAGGACAAAAACTGGCCCCCATTTATCCCCATCCTTCATCATGATATTGCCAGGGACATACCGTCACACACACAACAACTGCAGTAMapped 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|25799630|gb|CA755591.1|CA755591EST: GAAATCAAAAGGAGAGAGGAGGCTGCAGCACGAG CTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCC
genomic: GAAATCAAAAGGAGAGAGGAGGCTGCAGCACGAGgtagagcttc ... agttttgcagCTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccctttgccttcatccctgtagatttgcactgctgatcttactagttttgcagCTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCCATAATGATATTGGCAATGAGATACCTGTCCACCTGCAAAGAACACAGTA
atcttac putative branch site (score: 3)
tagattt 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
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gtagagcttctgttttgttgtcatcatttttttctttcttgttgccctttgccttcatccctgtagatttgcactgctgatcttactagttttgcagCTGGTATTGTGTTGGAAGACAAAAACTGGCCTCCATTTTTCCCCATCATCCATAATGATATTGGCAATGAGATACCTGTCCACCTGCAAAGAACACAGTA
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