Sequence
atgc intronic sequence ATGC exonic sequence...ttgaggttgtaactaataatgcatggacctagtgttgtaattccatatgattggtaagttggtagttaccgatgctcatatctaatgcaactgtttccagAATGAGTTTGGTGTTTGGGAGATTTTTCTGCCTAACAATGCTGATGGCTCATCTCCTATTCCACATGGCTCACGTGTAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32660.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 6
ttgaggttgtaactaataatgcatggacctagtgt-tgtaattccatatgattggtaagttggtagttaccg-atgctcatatctaatgcaactgtttc---cagAATGAGTTTGGTGTTTGGGAGATTTTTCTGCCTAACAATGCTGATGGCTCATCTCCTATTCCACATGGCTCACGTGTAAAG
| ||| |||| || || || ||| ||| | | | | | || || | | || || || | | | | | ||| ||||||||||||||||||||||| |||||||||||||||||||| ||||| |||| |||||||| ||||| || |||||||||
----taatataa-taatgatacacaactctcttgtatgttagcgaaaaaaaaagaaaacttactgatcctcgcatagtctaaatcgaggtactttgttcttgcagAATGAGTTTGGTGTTTGGGAAATTTTTCTGCCTAACAATGCAGATGGTACATCACCTATTCCTCATGGATCTCGTGTAAAG
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 6
--ttgaggttgtaactaataatgcatggac--ctagtgtt--gtaattccatatga--ttggtaagttggtagttaccgatgctca--tatctaatgcaactgtttccagAATGAGTTTGGTGTTTGGGAGATTTTTCTGCCTAACAATGCTGATGGCTCATCTCCTATTCCACATGGCTCACGTGTAAAG
|| | | |||| | ||| | | || || | ||| | ||| ||| || | || | | | | || | ||| || || || |||||||| ||||||||||||||||| ||| |||| ||||| ||||||| || || | ||||| ||||||||||||||||||
gtatggcctactgactactt-tgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------ttgaggttgtaact-aataatgcatgg-acctagtgttgta-attccatatgattggtaagttggtagttaccgatgctcatatctaa--------tgcaactgtttc-----cagAATGAGTTTGGTGTTTGGGAGATTTTTCTGCCTAACAATGCTGATGGCTCATCTCCTATTCCACATGGCTCACGTGTAAAG
|| | || || | || | ||| || | || | | | || || || | || | | || |||||| | |||||| | ||||| || |||||||| ||||| || |||||||| || ||||||||||||||| | | ||||| |||||||| ||||| |||
gtatgctcacacactctaatttgtgatctattgtttaatcttccgtcttagcttataatttggctagaagttaaatttttacttgaaccttaaatgatacttgttggcgcatgctttgctctgttattattctgttcctttctggaattctgatctaagactgtcttacaactgatatttgagcagAACGACTTTGGTGTGTGGGAAATATTTCTGCCAAATAATGCTGATGGCTCACCAGCAATTCCCCATGGCTCCCGTGTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgattggtaagttggtagttaccgatgctcatatctaatgcaactgtttccagAATGAGTTTGGTGTTTGGGAGATTTTTCTGCCTAACAATGCTGATGGCTCATCTCCTATTCCACATGGCTCACGTGTAAAG
atctaat putative branch site (score: 3)
ctgtttcc putative PPT
atatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaggttgtaactaataatgcatggacctagtgttgtaattccatatgattggtaagttggtagttaccgatgctcatatctaatgcaactgtttccagAATGAGTTTGGTGTTTGGGAGATTTTTCTGCCTAACAATGCTGATGGCTCATCTCCTATTCCACATGGCTCACGTGTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT