Sequence
atgc intronic sequence ATGC exonic sequencegtagccagacatgttttccctcacaattaaactgtaaaagaggcatcttgctttctgtagctaaatttatgtctgattttacttgttgtaagATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g04200.1 (Oryza sativa), 3'ss of exon 4
------------------------------------gtagccagacat-gttttccctcacaattaaactgtaaaagaggcatcttgctttctgtagctaaatttatgtctgattttacttgttgtaagATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
| | | ||| ||||| || || | ||| | | |||| | | ||| ||| ||| || || ||||| | ||| ||| | | || || | ||||||||||||||||| || | |||||||||||||||| || ||||| || |||||||| || |||||||| |
gtaatatataatatgtttatccattcattagtttctagaacaaaacaaagttttaactttgaactgttctgctattaaatcatca-gttcatggtaaagaaacc---acttgaaatt--ttcttgtagGTTAA-TGCTTCCAGCAGACCCAAAAATAGTGCTCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCAGTAATCACTGAGGAAGTCACTG
upper sequence: AT5G66540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g04010.1 (Oryza sativa), 3'ss of exon 4
------------------------------------gtagccagacatgttttc--cctcacaattaaactgtaaaagaggcatcttgctttctgtagctaaatttatgtctgattttacttgttgtaagATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
| | | ||| |||| | | || | ||| | | |||| ||| ||| ||| ||| || || ||||| | ||| ||| | | || || | || |||||||||||||| || | |||||||||||||||| || ||||| || |||||||| || |||||||| |
gtaatatataatatgtttatccattcattagtttctagaacaaaacagatttttaactttgaaactgttctggtattaaatcatca-gctcatggtaaagaaacc---acttgaaatt--ttcttgtagGTTAA-TGCTTCCAGCAGACCCAAAAACAGTGCTCTAGAAGTGGACCTTGATTTTGAGCACAATGTAAGACCTGCCCCAGTAATCACTGAGGAAGTCACTG
upper sequence: AT5G66540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G09590.1 (Glycine max), 3'ss of exon 5
--------gtagccagacatgttttccctcacaattaaactgtaaaagaggcatcttgctttctgtagctaaatttatgtctgatt-ttacttgttgta--------agATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
|||| | | |||| | ||| ||| | |||| | | ||||| | ||| |||| || |||||| | || ||||||| |||||||| |||| ||||||||| | ||||||||| | || |||||||| |||| |||||||||||||||||||| |||||||| ||||
gtaatacagtagtcccttacttttttttacctgatttttttgtggattgcattccttggccctttttgctaatatggtgttagattattgattgttgaatttataacagGTAACTGCTGCAAAGAGACCAAAGAATAGTGCATTGGAAGTTGATCTGGACTTTGAGCATAATGTGAGGCCTGCTCCTGTAATCACTGAAGAAGTTACAG
upper sequence: AT5G66540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G02340.1 (Glycine max), 3'ss of exon 4
--------gtagccagacatgttttccctcacaattaaactgtaaaagaggcatcttgctttctgtagctaaatttatgtctgatt-ttacttgttgta--------agATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
|||| | | | |||| | ||| | || | ||| | ||||||| | ||| ||| ||| |||||| | || ||||||| |||||||| || | ||||||||| | || |||||| | || ||||||||||||| |||||||||||||||||||| |||||||| ||||
gtaatacagtagtccccctttttttttacc-tgatttattcgttggttgcatttgttggcccttttagctaatatggtgttgcattattaattgttgaatttataacagGTAACTGCTGCAAAGAGACCCAAGAATAGTGCATTGGAGGTTGATCTGGACTTTGAGCACAATGTGAGGCCTGCTCCTGTAATCACTGAAGAAGTTACAG
upper sequence: AT5G66540.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g08620.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------gtagcca-gacatgttttccctcacaattaaactgtaa---aagaggcatct-tgctttctgtagctaaatttatgtctg---attttacttgttgta---agATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
||| | || | || ||| | ||| ||| | | | || | || ||| | | ||||| ||| | ||| || ||| || ||||||| || || ||||||| |||||||||| ||||||||||| |||||||||||||||||| || ||| |||||||||||||||| || || ||||
gtaaccttttttgtttctgacatttttgtgttagagatgaattacatttattcaaatgcaaagtgtgctttgatatgaatgtgtgtttttaaaatatgaatttgacactgcttactttggtttttgattgcagGTAACTGCTGCTAAAAGGCCAAAGAATAGTGCTTTAGAAGTTGATCTAGATTTTGAGCACAATGTGAGACCTCCTCCTGTAATCACAGAGGAGGTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaggcatcttgctttctgtagctaaatttatgtctgattttacttgttgtaagATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
ttttactt CT-rich tract
taaatttatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagccagacatgttttccctcacaattaaactgtaaaagaggcatcttgctttctgtagctaaatttatgtctgattttacttgttgtaagATAACTGCGGCAAAGAGGCCAATGAATAGTGCTCTAGAAGTTGATTTAGATTTTGAGCACAATGCCAGGCCTGCTCCTGTAATCACAGAAGAAGTCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT