Sequence
atgc intronic sequence ATGC exonic sequencegtaagcattcccaactattagaatttaatacacagaccagattttatattattgcctcatgatattacctcttgctttttatgtcccttcttcttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G14270.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 4
gtaagcattcccaactattagaatttaatacacagaccag-attttat---attattgcctcatgatattacctcttgctttttatgtc------ccttcttcttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
| || || | || ||||| | | || | |||| | |||| | || | ||| || | || | | ||| |||| ||||| | || || |||| |||||| ||||||||||||||||||| || || |||||||| |||||||| ||||| ||||| || |||||||| |
-------cgcttcacgatcaacgtt-aatacttactctagtactttacgaaagaattgaataataaaattgaagtcaatttcatgtgctaactattcctaatctgtagATATTGCTCAAAGGAGCTAATGGCGATGAGCTGAAAAAAGTGAAGCATGTTGTGCAATATGGAGTCTTTGCAGCCTATCACTTGGCTCTGGAAACATCTT
upper sequence: AT3G14270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 4
gtaagcattcccaactattagaatttaatacacagaccagattttatattattgcctcatg-atattacc-tcttgctttttatgtcccttctt-cttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
|| | | | | | | | | || | | || | || | | | | || |||| || | | | | ||| | | || |||| ||||| | ||||| |||| |||||| | ||||| ||||||||||| | || |||||||| |||||||| || ||||||||||| |||||||| |
gtttgt-tccttgaatgctttattaggccactttggcatcatctcatgtaaataaatgatctgcattatggtcatatatctaacttcctctgatgctgtagATCTTGCTTAAAGGTGCTAATGGTGATGAGCTAAAAAAGGTGAAGCATGTTTTGCAATATGGAGTATTTGCAGCCTACCATTTGGCACTTGAAACATCAT
upper sequence: AT3G14270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G01590.1 (Glycine max), 3'ss of exon 6
-gtaagcattcccaactattagaatttaatacacagaccagattttatattattgcc-tcatgatattacctcttgctttttatgtcccttcttcttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
||| ||| ||| ||| | | || | | | || | | | | | || | | || | | || || |||||||| || | ||||| | | ||||| ||||| || || ||||||||||| |||||||||||||||||||||||||||||||| | || ||||| |
aataatcatctaatactcttactttagatggcattttattgtaaacaagtaatggagaccgtatgaagagttcatttatcttgtatttctaattgaacagATTTTACTTAAAGGTGCTGACAAGGATGAATTGAAGAAGGTAAAGCATGTGGTTCAGTATGGAGTTTTTGCAGCTTATCATTTGGCTTTGGAGACATCTT
upper sequence: AT3G14270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G05100.1 (Glycine max), 3'ss of exon 4
--gtaagcattcccaactattag--aatttaatacacagaccagattttatattattgcctcatgatattacctcttgctttttatgtcccttcttcttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
| || | ||||| | | | | | | || | |||| | || | | || ||| || || |||||||| || | ||||| | | ||||| ||||| || || || |||||||| ||||||||||||||||||||||| |||||||| | || ||||| |
catctaatatgtttagttattatttagatggaattttattgtaaacaagtaatggagactgtatgaag--agttcatttatcttgtgtttctaattgaacagATTTTACTTAAAGGTGCTGACAAGGATGAATTGAAGAAGGTAAAACATGTGGTTCAGTATGGAGTTTTTGCAGCTTACCATTTGGCTTTGGAGACATCTT
upper sequence: AT3G14270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g00380.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------gtaagcattcccaactattagaattt--aatacacagaccagattttatattattgcctcatgatattacctcttgctttttatgtcccttcttcttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
| || || | ||| | || |||| || | ||||| ||| | | ||| ||| | ||| || ||| | ||| | |||||||| || |||||||| ||| ||||| ||||| |||||||||||||| |||| |||||| ||||||| || ||||| ||||| | || || || |
gtaagttcaaacttcccgtgcttgtggaaagtatttaaatttgttattagtggaccatgcaattgaaccttctaata-actaagttgatttgatagaccttctacatagaatt-catctggcccttttctttttatctattgcagATTTTACTTAGGGGTGCTAATAGGGATGAATTGAAGAAAGTGAAGCATGTAATCCAATATGGAATTTTTGCTGCCTATCACTTGGCTTTGGAGACGTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatattattgcctcatgatattacctcttgctttttatgtcccttcttcttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
tattacctcttgcttt CT-rich tract
atgatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcattcccaactattagaatttaatacacagaccagattttatattattgcctcatgatattacctcttgctttttatgtcccttcttcttcagATTTTGCTGAGGGGTGCAAATGAAGATGAGTTGAAAAAAGTGAAGCATGTGGTCCAGTATGGAGTTTTTGCAGCTTATCATTTGGCACTCGAAACATCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT