Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagtttacctaaagtttgattcagcgctcattgacttttgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 3
gtaaaagtttacctaaagtttgattcagcgctcattgacttttgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
||||| | || |||| || | || | |||| || ||| | || ||| |||| || | ||| ||||||||||||| || |||| || ||| ||||||||||| ||||| ||| | ||||| || ||||||||||| || ||||||||||||||||| |||||||
gtaaacaaatgaacaaggttttgttaataaagtat--atctttgctgtagcttttttaccaa----tga--agctaatgcaagtgtat----ggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAACAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
gtaaaagtttacctaaagtttgattcagcgctcattgacttttgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
||||| | || |||| || | || | |||| || ||| | || ||| |||| || | ||| ||||||||||||| || |||| || ||| ||||||||||| ||||| ||| | ||||| || || |||||||| || ||||||||||||||||| |||||||
gtaaacaaatgaacaaggttttgttaataaagtat--atctttgctgtagcttttttaccaa----tga--agctaatgcaagtgtat----ggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
upper sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 3
gtaaaagtttacctaaagtttg-attcagcgctcattgacttttgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
|||| | | ||| |||| | | | | || || | || | | | | | || |||| || | || ||||||||||||||| || |||| ||| ||| || |||||||| |||||||| | ||||| || ||||| ||||| | || |||||||||||||| |||||||
gtaaccaagtgcagaaattttggaattgcaagtagatctctgttatttctgcaact-gtttgacatctaggaagctaatgc---taagtttatggcagGAAGGTATATCACTTTTTAACAGGAAGCCGAAGAAAGGAATTGAATTCCTCATCAATGCCAACAAAGTGGGTAATTCACCAGAGGAAATAGCTGCTTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
tattaat putative branch site (score: 2)
tttttatt CT-rich tract
tgatttgtttttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagtttacctaaagtttgattcagcgctcattgacttttgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT