Sequence
atgc intronic sequence ATGC exonic sequencegtaaacaacattaaagccaaaagcatcgatttgataagcatcagttggttaaccaaaatgttttgctcctttctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39660.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 7
-----gtaaacaacattaaagccaa--------aagcatcgatttgataagcatcagttggttaaccaaaatgttttgctcctttctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
|| | |||| | | | |||| | ||| || | | | | || ||| | | | | | ||||||||| || | || || || ||||||||||||||||| || ||||||||||| |||||||||||||||||| | |||||||||||||
gttacacaagaaccattttattctatgcatgtgaagccttattttccaaaataacttccaaacagtcttaacaatttatttgtatatgc-attgaagAACTCGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14850.2 (Glycine max), 3'ss of exon 7
--------gtaaacaacattaa-------agccaaaagcatcgatttgataagcatcagttggttaaccaaaatgttttgctcctttctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
||| | ||| | || || | || || | || | | | || | || | | | | | | |||||| ||||| | || || || ||||||||||||||||| || ||||||||||| |||||||||||||||||| | |||||||||||||
gttagacaaggaaccattttattttatgcatccgaagccttcttttccaaaaataacttccaaaccgtctaa-cgaattatttgtatat-tcattgaagAGCTTGGTGTGCTAGTTGGGAAAGGAGGACTTCATGGCAATGTTTTCAGGATCAAGCCACCAATGTGTTTCTCCAAAGATGATGCAG
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G36000.2 (Glycine max), 3'ss of exon 7
gtaaacaacat--taaagccaaaagcatcgatttgataagcatcagttggttaac-----caaaatgtt----ttgctcctttctcttaat-gaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG-------------
|||| || | | | ||||| || | | | || || || ||||| | || | | || | ||| | ||| || || ||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||||| |||||||||||||
gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAGGTATATAAATAAA
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 7
gtaaacaacat--taaagccaaaagcatcgatttgataagcatcagtt-----ggttaaccaaaatgtt----ttgctcctttctcttaat-gaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
|||| || | | | ||||| || | | | || || || ||||| | || | | || | ||| | ||| || || ||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||||| |||||||||||||
gtaagaaatttggttgaataaaaagaattgcatatgaagctttcttttccaaaatttctacaaaacatagtaactgtttactcctataaattgtagAGCTCGGTATTCTAGTTGGAAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G02440.1 (Glycine max), 3'ss of exon 9
gtaaacaacat--taaagccaaaagcatcgatttgataagcatcagtt-----ggttaaccaaaatgttttg-ctcctttctcttaatga----agAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
|||| || | | | |||| || | | | || || || ||||| | | || || ||| || | ||| || || ||||| || || |||||||| || ||||| || ||||| ||||| |||||||||||||||||||| |||||||||||||
gtaagaaatttggttgaataaaaaaaattgcatatgaagctttcttttccaaaatttctacaaaacatggtaactgtttactcctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
gtaaacaacattaaagccaaaagcatcgatttgataagcatcagttg--gttaaccaaaatgtt--ttgctcctt--tctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
|| | | ||| |||| || || | ||| || ||||| | | || | || | | | | || ||| | || ||||| ||||||| |||||||| ||||| || || ||||| ||||||||||| ||||||||||| ||||||||||| |
---------gtttgcaactccaccat-gattaagaaaaaattaattgtaatttaccaacacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgataagcatcagttggttaaccaaaatgttttgctcctttctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
tcttaat putative branch site (score: 3)
tgttttgctcctttct CT-rich tract
aaaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacaacattaaagccaaaagcatcgatttgataagcatcagttggttaaccaaaatgttttgctcctttctcttaatgaagAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG