Sequence
atgc intronic sequence ATGC exonic sequencegtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16950.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
||||||| | | || || | |||| | | || | ||| || | | | || |||| |||| || |||||| |||| || || || | | | ||||| || ||||||||||||||||| || ||||| ||||| ||||| ||||| || || |||||
gtaaatgttgtgctcacctgtttcttttatccatgc---------tcgatgctgatcactatagttcttatacgagc-----aaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 10
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
||| || || ||| | || | || || | | || | || | || || | | ||| ||||||| || ||||| | ||| |||||||| ||||| |||||| | ||||| ||||||||||| || ||||||||||||||||||||||| ||||| |||||
---------------gtaagaagcaggtaatgtaattttgctactaatttttgagtcatttgcttccatttacttaatgaaaagattgt------tggatagTGGTTGAACAAGTGACCGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 10
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
| | | || || | |||||||| | || | || | || | ||| | | |||||| || ||||||| || ||||||| ||||| |||||| | ||||||||||||||||| || ||||||||||||||||||||||| ||||| |||||
----------------------gtaagtggtaactca-tgtaattttcccaaaaattttagtttttgctgcaatatcatttgatgaaaaaattgtctaacagTGGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGA
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
||| || || | ||| || ||| | | | ||| || | || | | | ||| | | ||| |||||| || ||||||| || |||||||| ||||| |||||| | ||||| ||||||||||| || ||||||||||||||||||||||| ||||| || ||
---------------gtaagaagcaagtaa---tgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 10
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
||| | || ||| | ||| ||| | ||| || || | ||| | ||| | ||| |||||| || ||||||| || | |||||| ||||| |||||| | ||||||||||||||||| || |||||||||||| | |||||||| |||||||||||
---------------gtaagtggtaactgatg------taacttttccaaaatttagtttatgcagca-atatcatttgatgaaaaaattgtctaa---cagTGGTTGAACAAGTCACTGGAAAAGATCACGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAACTTAGCATGGTTGGATTAACAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
ctcttac putative branch site (score: 3)
ctcttactct CT-rich tract
ttgtattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG