Sequence
atgc intronic sequence ATGC exonic sequence...cttctagaaaagtgataacatgttttgacttatatgattgatgatatttttgtgaaatgatttttgacaactagacgggattttgtttgttcacatgcagGCTATTGATCCAAGAACACGCATGGTTCTGTTCAAGATGTTAAACCGGGGGGTTTTTAATACCATAAATGGGTGCATTTCTACAGGGAAAGAG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os07g06820.2 |
| intron # | 6 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 2
--cttctagaaaagtgataacatgttttgacttatatgattgatgatatttttgtgaaatgatttt-tgacaactagacgggattttgtttgttcacatgcagGCTATTGATCCAAGAACACGCATGGTTCTGTTCAAGATGTTAAACCGGGGGGTTTTTAATACCATAAATGGGTGCATTTCTACAGGGAAAGAG
||| | | | ||| | | || || | || | | ||||| | || ||||| ||| ||| | | ||||||||| | |||||||||||||| |||||||||||||||||| | ||||||||||||||||| || || ||||||| ||||||||| |||||||||||||||||||||
gtcttaaaaataggtgtgagttggcttaccgaaatctaatgaaggttatttcaattgaaccattttctgaacactgaatgtt-ttttgtttga--atatgcagGCTATTGACCCAAGAACACGCATGGTTTTATTCAAGATGTTAAACCGTGGTGTCTTTAATAACATAAATGGCTGCATTTCTACAGGGAAAGAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 4
cttctagaaaagtgataacatgttttgacttatatgattgatgatatttttgtgaaatgatttt-tgacaactagacgggattttgtttgttcacatgcagGCTATTGATCCAAGAACACGCATGGTTCTGTTCAAGATGTTAAACCGGGGGGTTTTTAATACCATAAATGGGTGCATTTCTACAGGGAAAGAG
| ||||| | || ||||| ||| ||| | | ||||||||| | |||||||||||||| |||||||||||||||||| | ||||||||||||||||| || || ||||||| ||||||||| |||||||||||||||||||||
------------------------------------------gttatttcaattgaaccattttctgaacactgaatgtt-ttttgtttga--atatgcagGCTATTGACCCAAGAACACGCATGGTTTTATTCAAGATGTTAAACCGTGGTGTCTTTAATAACATAAATGGCTGCATTTCTACAGGGAAAGAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G166018_T01 (Zea mays), 3'ss of exon 2
-cttctagaaaagtgataacatgttttgactta-tatgattgatgatatttttgtgaaatgatttt-tgacaactagacgggattttgtttgttcacatgcagGCTATTGATCCAAGAACACGCATGGTTCTGTTCAAGATGTTAAACCGGGGGGTTTTTAATACCATAAATGGGTGCATTTCTACAGGGAAAGAG-------
||| |||| | | | || || | | | | || | | ||||| | || ||||| ||| ||| | | ||||||||| | |||||||||||||| |||||||||||||||||| | ||||||||||||||||| || || ||||||| ||||||||| |||||||||||||||||||||
ttgtcttaaaaataggtgagttgccttaccgaaatctaatgaaggttatttcaattgaaccattttctgaacactgaatgtt-ttttgtttga--atatgcagGCTATTGACCCAAGAACACGCATGGTTTTATTCAAGATGTTAAACCGTGGTGTCTTTAATAACATAAATGGCTGCATTTCTACAGGGAAAGAGGTAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttgtgaaatgatttttgacaactagacgggattttgtttgttcacatgcagGCTATTGATCCAAGAACACGCATGGTTCTGTTCAAGATGTTAAACCGGGGGGTTTTTAATACCATAAATGGGTGCATTTCTACAGGGAAAGAG
ttttgac putative branch site (score: 3)
tttgttc putative PPT
aaatgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttctagaaaagtgataacatgttttgacttatatgattgatgatatttttgtgaaatgatttttgacaactagacgggattttgtttgttcacatgcagGCTATTGATCCAAGAACACGCATGGTTCTGTTCAAGATGTTAAACCGGGGGGTTTTTAATACCATAAATGGGTGCATTTCTACAGGGAAAGAG
- -ctagaaaa
- - - - - - - - aacatgt
- - - - - - - - - - - - - - - - - - -ttgatga
