Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgaacttactgtgagactttacaacaaatttaccttttctttcaattgtagtctcttcacttatctcaatattttctataagttctcatagatccctgatctatttttcataattatctgcatgtatttagGTATTTGACAGCGTTCATCCTCCTCTGGAAGTTGAATAGCAAAATAGTTCTGTTCTCATGGAATATTGTTTCTGGAGACATCATCCGCTACCTAAAATCT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g01580.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G150557_T01 (Zea mays), 3'ss of exon 2
gtatgttgaacttactgtgaga-ctttacaa-caaatttaccttttctttcaattgtagtctcttcacttatctcaatattttctataagttctcatagatccctgatctatttttcataattatctgcatgtatttagGTATTTGACAGCGTTCATCCTCCTCTGGAAGTTGAATAGCAAAATAGTTCTGTTCTCATGGAATATTGTTTC---TGGAGACATCATCCGCTACCTAAAATCT
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gtatgttgatgccatcgtgatatccttataaataaaatgagattttctt--acttggagtatctatgcctctattataattatctaa-----cttatagttgtctaaagtattttt-----ttgtctacatgtattcagGTACCTGACAGCATTCATCCTCCTTTGGAAGCTGAATAATGAAGTAGATCTGTTCTCATGGAATATAATTGAGGATGGAGGAGTCATCCGCTACCTGAAA---
upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G890665_T02 (Zea mays), 3'ss of exon 5
gtatgttgaacttactgtgagactttacaacaaatttaccttttctttcaattgtagtctcttcacttatctcaatatt-ttctataagttctcatagatccctgatctatttttcataattatctgcatgtatttagGTATTTGACAGCGTTCATCCTCCTCTGGAAGTTGAATAGCAAAATAGTTCTGTTCTCATGGAATATTGTTTCTGGAGACATCATCCGCTACCTAAAATCT
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gtatgttgatgccatcat-attcttataaataaaataatattttctt--atttggagtatctttgcctctgttgttattattatctaa---cttgtaattattgaaagtatttatattttttgtctacatgtacttagGTACTTGACAGCAATCATCCTCCTTTGGAAGTTGAATGATGAAGTAGATCTATTGTCATGGAATATAATTGAGGATGGAGTCATCCGCTACCTGAAATCTMapped 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|570085|gb|D40934.1|D40934EST: CCACTTGGTCTAGGAGTAAGTGGCGCTGCATTGGCAACAGTGACTTCTGA GTATTTGACAGCGTTCATCCTCCTCT
genomic: CCACTTGGTCTAGGAGTAAGTGGCGCTGCATTGGCAACAGTGACTTCTGAgtatgttgaa ... atgtatttagGTATTTGACAGCGTTCATCCTCCTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataagttctcatagatccctgatctatttttcataattatctgcatgtatttagGTATTTGACAGCGTTCATCCTCCTCTGGAAGTTGAATAGCAAAATAGTTCTGTTCTCATGGAATATTGTTTCTGGAGACATCATCCGCTACCTAAAATCT
ccctgat putative branch site (score: 4)
tgatctatttttcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgaacttactgtgagactttacaacaaatttaccttttctttcaattgtagtctcttcacttatctcaatattttctataagttctcatagatccctgatctatttttcataattatctgcatgtatttagGTATTTGACAGCGTTCATCCTCCTCTGGAAGTTGAATAGCAAAATAGTTCTGTTCTCATGGAATATTGTTTCTGGAGACATCATCCGCTACCTAAAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA