Sequence
atgc intronic sequence ATGC exonic sequence...gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g18030.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttg-----tgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
|| | | || | |||||| || | || || | || | | | || || | || || | || ||||| ||| |||| ||||| | || | | | | || | || || | || | |||| || |||||||| ||||| ||||||||||| |||||||| ||||| | || ||||| |||
-ttta-gctaagcctagatttattgtttgatggaagtgtt-tctttattaatctagttctcgtcataaca-aacttaaattattgaattttgttgtatttat-agTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG
upper sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
gttaatggtattcaaagatttgttttatgttgaattaattatttctgt-tgataggatccttttctttttgtaatgtaaatg--cttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
| | ||| || || | | | ||| | ||| | | || | | || | | | | |||| ||| || || | | ||| | |||| || | || || | || || ||||| ||||||||||| ||||| || |||||||| |||||||||||||| | || ||||| |||
--ttgtaaaatttaatgaagcctagatctgtaatttatatgtttattcattatctagttactgtcatcataaactttaaacaactttgcttttcatctat-agAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
upper sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
---------gttaatggtatt-caaagatttgttttatgt-tgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
| |||||| || |||| | | |||| | | ||| ||||| | ||| | ||| | |||| || ||| || |||| ||| | |||| || | ||||| | || ||||| || ||||||||||| ||||| || ||||| || |||||||||||||| | || ||||| |||
ccttcattcatgaatggtttttcaaaaaccattcttatatgtttatttattatcta-gttactgtcatcataaactttacacaac-------tttgcatttcattt---agAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
upper sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttg-----tgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
|| | | || | |||||| || | || || | || || | || || | || || | || ||||| ||| |||| ||||| | |||| | | | || | ||||| | || | ||||| ||||||||||| ||||| ||||||||||| |||||||||||||| | || ||||| |||
-ttta-gctaagcctagatttattgtttgatggaagttttgatt-tattcatctagttctcgtcataaca-aacttaaattattgaattttgttgtatttat-agAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
upper sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgatagg--atccttttctttttgtaatgtaaat-gcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
| | || || | | ||| | ||||| | || |||||| | || | | ||| ||| || | || | | | ||| | | ||| | ||| |||| | || | || || | ||| ||||| || ||||||||||| | || ||||||||||| |||||||||||||| | || || || |||
-cttacattactctacg--ttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
upper sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
------gttaatggtattcaaagatttgttttatgttgaattaat-tatttctgttgataggatccttttctttttgtaatgtaaatgcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
|| || ||| | | || || | | | |||| || |||| | | ||| ||||| || | | ||| | ||| |||||| || || || || | || |||||||| |||||||||||| | || || || ||||| |||||||| |||||| | || |||||||||
atgtatctttgtgatatctggttaatctttctacttgatgccagtgtattcagaccagta--atccaggatgtgt--taacctaaatatttatctgttatgt---agAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgataggatccttttctttttgtaatgtaaatgcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
tgttgat putative branch site (score: 4)
ttttctttttgtaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatggtattcaaagatttgttttatgttgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT