Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgagaaacatatggatgaaagcgtaatgagaatagttgtggtgtggaaattttctatttattcatgcttatcctttgaaatgatatttttcaattagCTGCTGGAGCTGGCTTGACGGGGAGCAAAATGGCCAGAAGAATTGGGAGCGTGAAAGAATTTGAGTTCAAACCTATTGGTGAAAACCATAATCAGGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G092776_T01 (Zea mays), 3'ss of exon 7
ttgtgagaaacatatggatgaaagcgtaatgagaatagttgtggtgtggaaattttctatttattcatgcttatcctttgaaatgatatttttcaa-ttagCTGCTGGAGCTGGCTTGACGGGGAGCAAAATGGCCAGAAGAATTGGGAGCGTGAAAGAATTTGAGTTCAAACCTATTGGTGAAAACCATAATCAGGGT
|| | ||| | | || |||| ||||||| |||| || || ||| | | | | ||||| |||| | ||| ||||||||||| |||||||||||||| | ||||||||| ||| ||||||| | |||||||||||||||||||||||||||||||| |||||||||||||
-agttaacttgtaatgcagtatccaaaaaagagatagaaagtggtgtacaaatgttgtacttagcttttaatgttcgttgaattgatttccgacaaattagCTGCTGGGGCTGGCTTGACGGGTACCAAAATGGCAAGACGAATTGGTAAAGTGAAAGAATTTGAGTTCAAACCTATTGGTGATAACCATAATCAGG--
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G092776_T04 (Zea mays), 3'ss of exon 7
ttgtgagaaacatatggatgaaagcgtaatgagaatagttgtggtgtggaaattttctatttattcatgcttatcctttgaaatgatatttttcaa-ttagCTGCTGGAGCTGGCTTGACGGGGAGCAAAATGGCCAGAAGAATTGGGAGCGTGAAAGAATTTGAGTTCAAACCTATTGGTGAAAACCATAATCAGGGT
|| | ||| | | || |||| ||||||| |||| || || ||| | | | | ||||| |||| | ||| ||||||||||| |||||||||||||| | ||||||||| ||| ||||||| | |||||||||||||||||||||||||||||||| |||||||||||||||
-agttaacttgtaatgcagtatccaaaaaagagatagaaagtggtgtacaaatgttgtacttagcttttaatgttcgttgaattgatttccgacaaattagCTGCTGGGGCTGGCTTGACGGGTACCAAAATGGCAAGACGAATTGGTAAAGTGAAAGAATTTGAGTTCAAACCTATTGGTGATAACCATAATCAGGGT
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
ttgtgagaaacatatggatgaaagcgtaatgagaatagttgtggtgtggaaattttctatttattcatgctta--tcctttgaaatgatatttt--tcaatt-agCTGCTGGAGCTGGCTTGACGGGGAGCAAAATGGCCAGAAGAATTGGGAGCGTGAAAGAATTTGAGTTCAAACCTATTGGTGAAAACCATAATCAGGGT
|| | | || ||| | | || | || | | | | | |||| | | ||| ||| |||| ||||||||| ||||| | || ||||| |||||||| ||||||| ||| || || | ||||||||||||||| ||||||| ||||||||||| || ||
-------------------------gtga-aacaactgttacattttttgggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggaaattttctatttattcatgcttatcctttgaaatgatatttttcaattagCTGCTGGAGCTGGCTTGACGGGGAGCAAAATGGCCAGAAGAATTGGGAGCGTGAAAGAATTTGAGTTCAAACCTATTGGTGAAAACCATAATCAGGGT
tatttttc CT-rich tract
tttgaaatgatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgagaaacatatggatgaaagcgtaatgagaatagttgtggtgtggaaattttctatttattcatgcttatcctttgaaatgatatttttcaattagCTGCTGGAGCTGGCTTGACGGGGAGCAAAATGGCCAGAAGAATTGGGAGCGTGAAAGAATTTGAGTTCAAACCTATTGGTGAAAACCATAATCAGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA