Sequence
atgc intronic sequence ATGC exonic sequence...agaagatgcaagtttgatcgttttcctttgatgcccttatctcaatatcttaaacacctatggtttcaagttatatttcttctgattttaatgcacacagGAAGTTATATATAGTTGATGCCCGGCCAAGAGCAAATGCTTTAGCAAATGGTGCAAAGGGAGGTGGCTCAGAGTCAGCATCAAACTACCCAAGATCTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g44260.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G449163_T01 (Zea mays), 3'ss of exon 2
agaagatgcaagtttgatcgttttcctttgatgcccttatctc-----aatatcttaaacacctatggtttcaagttatatttcttctgattttaatgcaca-cagGAAGTTATATATAGTTGATGCCCGGCCAAGAGCAAATGCTTTAGCAAATGGTGCAAAGGGAGGTGGCTCAGAGTCAGCATCAAACTACCCAAGATCTGAG
|| |||||| | | || || ||| | |||| | | | | ||| || | | || |||| | ||| | | |||||| || || ||| |||||||||||||||||||||||||| |||||||||| ||||||||||| |||||||| ||| | || ||||||| | |||||||
---ccattattctttgatgctctctctaaaccacctttactttttttggatattatccataataaaaattttaaatagtgcttattct---cctgatgtaaaacagGAAATTGTACATAATTGATGCCCGGCCAAGAGCAAATGCTATAGCAAATGGGGCAAAGGGAGGGGGCTCAGAATCATCTTCTAACTACCATAAATCTGAG
upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 10
agaagatgcaagtttgatcgttttcctttg--atgccctt--atctcaatatcttaaacacctatggtttcaagttatatttcttctgattttaatgcacacagGAAGTTATATATAGTTGATGCCCGGCCAAGAGCAAATGCTTTAGCAAATGGTGCAAAGGGAGGTGGCTCAGAGTCAGCATCAAACTACCCAAGATCTGAG
| || | | | || | || | || ||| || || | ||| || | | | | | || | | |||| ||| || |||||| | ||||| || ||||| | || || |||||| ||||||||||| ||||||||||| |||||||| ||| | ||||| || ||||||
ataaaaaaatactctgctgtttcatatctgcaatgtggttgaatgttgatacct-ggttattaaaaatattca--cgtactctcctttgtttttatgt-catagGAAGCTTTATATCGTAGATGCAAGACCTAGGAAAAATGCATTAGCAAATGGAGCAAAGGGAGGAGGCTCAGAATCATCTTCAAATTATTTGCAATCTGAA
upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv13s0074g00300.t01 (Vitis vinifera), 3'ss of exon 10
-agaagatgcaa-gtttgatcgttttcctttgatgcccttatctcaatatcttaaacacctatggtttcaagttatatttcttctgattttaatgcacacagGAAGTTATATATAGTTGATGCCCGGCCAAGAGCAAATGCTTTAGCAAATGGTGCAAAGGGAGGTGGCTCAGAGTCAGCATCAAACTACCCAAGATCTGAG
||| || | | | | | ||| | | | | | | | ||| | | ||| |||| | | | | | |||||| ||||||| | |||||| | || ||| ||||||||||||||| || |||| |||||||||||||||||| | || | || ||||||
ggctgaatgaaatggtcttttaaatgatataaatgtatgtgtgtgcgcacttgtactatgtatattgtgggatta-atttaatgaagtgtcact-tttttagGAAGCTATATATCGCTGATGCAAGACCTAGAAAAAATGCTTTAGCAAACGGAGCAATGGGAGGTGGCTCAGAGTCCTCTTCTCATTATTTTCAGTCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcttaaacacctatggtttcaagttatatttcttctgattttaatgcacacagGAAGTTATATATAGTTGATGCCCGGCCAAGAGCAAATGCTTTAGCAAATGGTGCAAAGGGAGGTGGCTCAGAGTCAGCATCAAACTACCCAAGATCTGAG
ttttaat putative branch site (score: 3)
ttatatttcttctgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaagatgcaagtttgatcgttttcctttgatgcccttatctcaatatcttaaacacctatggtttcaagttatatttcttctgattttaatgcacacagGAAGTTATATATAGTTGATGCCCGGCCAAGAGCAAATGCTTTAGCAAATGGTGCAAAGGGAGGTGGCTCAGAGTCAGCATCAAACTACCCAAGATCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - -atgcaag
- - - - - - - - - - - - - - tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - -aaacacc