Sequence
atgc intronic sequence ATGC exonic sequencegtgtgaatacaaaatcagtgttagattacctgctactttgtatcgatgtaaatctttacaaatgtatttgtgtttctttcaatttcagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58870.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA0028S00210.2 (Glycine max), 3'ss of exon 5
gtgtgaatacaaaatcagt-gttagattacctgctactttgtatcgatgtaaatc-ttta----caaatgtatttgtgtttctttcaat-ttcagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
|| | || | | | || | ||| | | | ||||||| || | || || |||| ||| || | ||||| | | |||||||||||||| || ||||| |||||||| ||||| | || ||||||||||||||| | ||||||||||||||||| |||||||||
gtataaaaatatattcttttgttgtgtgaaat--cactttgt-tcaacatatattatttaatattaaactgatcaacatatcttttggtatgcagATAGATGCTGTGGCTAAAAGTCGTGATGGAAAATTTCGCATTGTCAGCAATGATGAACGAGAGCAAACCTTGAATCAGTTGCTCACT
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 5
gtgtgaatacaaaatcagtgttagattacctgctactttgtatcgatgtaaatc-ttta----caaatgtatttgtgtttctttcaattt-cagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
|| | || | | | | || | | ||| || | || || |||| ||| || | ||||||| | | |||||||||||||| || ||||| |||||||| ||||| | || ||||||||||||||| | ||||||||||||||||| |||||||||
gtataaaaatatatattcttttgttgtgtggaatcacttggttcaacatatattatttaatattaaactgatcagcatttcttttggtatgcagATAGATGCTGTGGCTAAAAGTCGTGATGGCAAATTTCGCATTGTCAGCAATGATGAACGAGAGCAAACCTTGAATCAGTTGCTCACT
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 6
gtgtgaatacaaaatcagtgttagattacctgctac-tttgtatcgatgtaaatctttacaaatgtatttgtgtttctttcaatttcagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
|| |||| | || || |||| | | |||| | || | | || ||| | || |||| | | |||||||||||||| || ||||| |||||||||||||| | || ||||||||||||||| |||| ||||||||||| || ||||||||
gtaagaatgtgtattc----ttttattatgtaagatgtttgatttaatattgactatt-caaccaagtaaactttcctttgatatgcagATAGATGCTGTGGCTAAAAGTCGTGATGGTAAATTTCGCATTGTCAGCAATGATGAACGGGAACAAACCTTGAACCAGCTGCTCACT
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 6
gtgtgaatacaaaatcagtgttagattacctgctactttgtatcgatgtaaatctttacaaatgtatttgtgtttctttcaatttcagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
|| ||||| | || || | || |||| | || | | || ||| | || |||| | |||||||||||||| || ||||| |||||||||||||| | || ||||||||||||||| | || ||||||||||| || ||||||||
gtatgaatgtgtattctttgatt--ctattaagatgtttgatttaatatttactatt-caaccaattaaactttccttttgtatgcagATAGATGCTGTGGCTAAAAGTCGTGATGGTAAATTTCGCATTGTCAGCAATGATGAACGAGAACAAACCTTGAACCAGCTGCTCACT
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgaat-acaaaatcagtgttagattacctgctactttgtatcgatgtaaatctttacaaatgtatttgtgtttctttcaatttcagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
|| ||| ||| |||| | | | | | | || | | | || | ||||| | | | |||||||||||||| || |||||||||||||||| ||| | || || ||||||||||| | |||||||||||||| || ||||| |||
gttagaaccgtggaatttttgttgtgtattcatgttcagcattttga-gcttcctggtgcgttgttagtcatgtttttcttcttcgcagATAGATGCTGTAGCAAAAAGCCGTGATGGTAGATTTCGCATTGTTAGCAATGATGAGCGAGAGCAAACCTTGAACCAGTTGCTTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactttgtatcgatgtaaatctttacaaatgtatttgtgtttctttcaatttcagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
tttgtgtttctttc CT-rich tract
taaatctttacaaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgaatacaaaatcagtgttagattacctgctactttgtatcgatgtaaatctttacaaatgtatttgtgtttctttcaatttcagATAGATGCTGTCGCGAAAAGCCGTGATGGTAAATTCAGAATGGTCAGCAATGATGAAAGGGAGCAAACCTTGAATCAATTGCTCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA