Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcagcaattggtccagtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g70300.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G300862_T01 (Zea mays), 3'ss of exon 10
gtatgttcagcaattggtccagtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
||||||| | || || ||| | ||| ||| | || || | |||||||| || |||||| |||||| |||| || ||||||| ||||||||| | |||||||| |||||||| ||||| |||||||||||| |||||||||| ||||||||||||||||||||||| |
gtatgttgaaca-ctgagccatt--tttgtatttatattacactgttctgatcactgcatgtatgaccttgagcagGTATTTGCTATATTTGAAGATCTATGTATATCTGTGGATTGTGTTGCTACCAGTGAAGTTAGTGTTTCTGTGTCACTTGATCCATCAAAGATCTGGAGTA
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G169046_T01 (Zea mays), 3'ss of exon 2
gtatgttcagcaattggtccagtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
||||||| | || | ||| | ||| ||| | || ||| | |||| ||| || ||| || |||||| |||| || ||||||| ||||||||| | |||||||| |||||||| ||||| |||||||||||| |||||||||| ||||||||||||||||||||||| |
gtatgttgaaca-ctaagccatt--tttgtatttatatttcactgttctaatcactgcatgtgtgaccttgagcagGTATTTGCTATATTTGAAGATCTATGTATATCTGTGGATTGTGTTGCTACCAGTGAAGTTAGTGTTTCTGTGTCACTTGATCCATCAAAGATCTGGAGTA
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G700866_T02 (Zea mays), 3'ss of exon 10
gtatgttcagcaattggtccagtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
||||||| | || || ||| | ||| ||| | || || | |||||||| || ||| || |||||| |||| || ||||||| ||||||||| | |||| ||| |||||||| ||||| |||||||||||| |||||||||| ||||||||||||||||||||||| |
gtatgttgaaca-ctgagccatt--tttgtatttatattccactgttctgatcactgcatgtgtgaccttgagcagGTATTTGCTATATTTGAAGATCTATGTATATATGTGGATTGTGTTGCTACCAGTGAAGTTAGTGTTTCTGTGTCACTTGATCCATCAAAGATCTGGAGTA
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G166366_T01 (Zea mays), 3'ss of exon 4
gtatgttcagcaattggtccagtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
||| ||| | | || ||| | ||| | ||| || ||| |||||||| || || ||| |||| |||| || |||||||| |||||||| | |||||||| |||||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||| | ||| |
gtacgttgaacg-ctgagccatt--tttgtactcatatttcaccgttctgatcactgcatgcatgacaatgagcagGTATTTTCTATATTTGAAGATCTTTGTATATCTGTGGATTGTGTTGCTACCAGTGAAGTTAGAATTTCTGTGTCACTTGATCCATCAAAGATTTTGAGTA
upper sequence: LOC_Os01g70300.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G866647_T01 (Zea mays), 3'ss of exon 5
gtatgttcagcaattggtccagtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
||||||| | || | ||| | ||| ||| | || ||||| |||| ||| || ||| || |||||| |||| || ||||||| ||||||||| | |||||||| |||||||| ||||| |||||||||||| |||||||||| ||||||||||||||||||||||| |
gtatgttgaaca-ctaagccatt--tttgtatttatatttcattgttctaatcactgcatgtgtgaccttgagcagGTATTTGCTATATTTGAAGATCTATGTATATCTGTGGATTGTGTTGCTACCAGTGAAGTTAGTGTTTCTGTGTCACTTGATCCATCAAAGATCTGGAGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
ttctgat putative branch site (score: 3)
tttaattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcagcaattggtccagtaattttaattcacatgtcattattctgatcgctctctgtatgcgcttgagaagGTCTTCTCTATATTCGAAGATCTAGGGATATCTGTAGATTGTGTGGCTACTAGTGAAGTTAGTATTTCTGTGTCGCTTGATCCATCAAAGATCTGGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA