Sequence
atgc intronic sequence ATGC exonic sequence...tactgttgatctaaaatgatttagacaaataagaaaacatattcaccctgttgaattgaatgttctttccaatttctgatgtatcggttacttttggcagGGCTTCAGGAAGGTGGATCCTGACAAGTGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTCCTTAAAAGCATAAAGCGTCGGAAACCTC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g58160.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g58160.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G132971_T01 (Zea mays), 3'ss of exon 1
tactgtt-gatctaaaatgatttagacaaataagaaaacatattcaccctgttgaattgaatgttctttccaatttctgatgtatcgg-ttactt---ttggcagGGCTTCAGGAAGGTGGATCCTGACAAGTGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTCCTTAAAAGCATAAAGCGTCGGAAACCTC
| | |||| ||||||||| || ||| | | ||| || || | |||| | ||| || ||| ||| || ||||||||||||||| |||||||||||||||| ||||||||||| ||||||| ||||||||||| |||| ||| ||||| |||| ||| | ||||||||||||||
--ttatccaatctgaaatgatttcagcagttaatt---cttcctcaatgaaaaatggcgattgatatttctggtgactggattagcggattatttggtttggcagGGCTTCAGAAAGGTGGATCCTGACAGATGGGAATTTGCTAATGAGGAGTTTCTGAGAGGTCAGAGGCACCTCCTCAAAAACATTAGGCGTCGGAAACCTC
upper sequence: LOC_Os03g58160.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G00560.1 (Glycine max), 3'ss of exon 1
tactgttgatctaaaatgatttagacaaataagaaaacatattcaccctgttgaattgaatgttctttccaatttctgatgtatcggt-tacttttggcagGGCTTCAGGAAGGTGGATCCTGACAAGTGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTCCTTAAAAGCATAAAGCGTCGGAAACCTC
||| | | ||| | ||| | || | || ||| || || || | ||| | | | | |||| || || ||||| ||||| || |||||||| ||||| ||||| || ||||| ||||||||||||||||| | || | ||||| | | ||| |
-ggggttcttaagatatgcctctctcaattcttttttgccatagtgatgataagatgttatggatttgaaaagaaggaataacttggtgttgtacttgtagGGGTTTAGAAAGGTAGATCCGGATAAGTGGGAGTTTGCTAATGAAGGGTTTCTTAGAGGACAGAAGCATCTATTGAAGAACATAAGGAGAAAGAAGACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctgttgaattgaatgttctttccaatttctgatgtatcggttacttttggcagGGCTTCAGGAAGGTGGATCCTGACAAGTGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTCCTTAAAAGCATAAAGCGTCGGAAACCTC
ttctgat putative branch site (score: 3)
ttactttt putative PPT
aattgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactgttgatctaaaatgatttagacaaataagaaaacatattcaccctgttgaattgaatgttctttccaatttctgatgtatcggttacttttggcagGGCTTCAGGAAGGTGGATCCTGACAAGTGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTCCTTAAAAGCATAAAGCGTCGGAAACCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC