Sequence
atgc intronic sequence ATGC exonic sequence...atattcttgatattgaagataaagtgtgaacttaggttatttttatggtgtaaaattaattaatggtacttagcttaatagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50150.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G19020.1 (Glycine max), 3'ss of exon 3
--atattcttgatattgaagataaagtgtgaacttaggttatttttatggtgtaaaattaattaatggtacttagcttaatagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
||| | || | || | | | || ||| | ||| ||| || | || | || | |||| ||| |||||||||| || || ||||||||||| || |||||||||||||| ||||| ||||| ||||||||||| || ||||| ||||||| | ||| || || || |
aaataaacaaattaattgccctatgttttttgcatattgaattgaagaatttctgtatttatttattg-acaaattgacatgcaccttaatgttat-tgcagCATGCAGTTGTTTTTGTAAATGGGGATCAATACTATGGAGCAAAAGCTAGCATAAACGTGTGGGCACCCCGTGTAACTGATGAATTTGAATTCAGCTTGT
upper sequence: AT5G50150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G09450.1 (Glycine max), 3'ss of exon 3
atattcttgatattgaagataaagtgtgaacttaggttatttttatg-gtgtaaaattaattaatggtacttagcttaa---tagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
| | | | | | || ||| | | ||| ||| || | | | | | ||| || | | | | |||||||||| || || | |||||||||||| |||||||||||||| ||||||||||| ||||||||| |||| | || || ||| | || || || ||||| |
--aataaaaggcctaagaacactgtaggaaa--aaatcattcccatgcatgcatatgtgtatgtttactgttaattttgatttttggcacacatcatgttgcagCATGCAGTTGTTTCTGTAAATGGAGATCAATACTATGGAGCAAAAGCAAGCATAAACGTGTGGACGCCTAGCGTAACCGATCCATACGAATTCAGTTTGT
upper sequence: AT5G50150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G02460.1 (Glycine max), 3'ss of exon 3
atattcttgatattgaagataaagtgtgaacttaggttatttttatg-----gtgtaaaattaattaatggtacttagcttaatagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
| || | ||| | | || ||| | || ||| | ||| | | | |||||| || || | | || | | | |||||||||| || || | |||||||||||| ||||||| |||||| ||||||||||| ||||||||| |||| | || |||||| | || || || ||||| |
aaataaaaggc-ctgagaacagtgtaggaa---aagtcattctcatgcatgcatatgtgtatgtttaatgataattttgatttttgacacacatcatgt-tgcagCATGCAGTTGTTTCTGTAAATGGAGATCAATACTTTGGAGCAAAAGCAAGCATAAACGTGTGGACGCCTAGCGTAACTGATCCATACGAATTCAGTTTGT
upper sequence: AT5G50150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g08870.t01 (Vitis vinifera), 3'ss of exon 3
atattcttgatattgaagataaagtgtgaac-ttaggttatttttatggtgta----aaatt---aattaatggtacttagcttaatagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
| | |||||| | |||| | | | || | | || | | ||| |||| ||| | ||| | | || | |||||||||| || || ||||| |||||||| || || |||||||| || || |||||||| ||||||||||| | || | ||| ||||| || || || |
------taagaaatgaagaaactgtgttcatgtcaaatttcactgaaactgcagtcgacattcagaattgtgggtgccccttttactgataatct--tttgcctgcagCATGCAGTTGTTTTTGTCAATGGAGATCAGTATTATGGAGCCAAGGCCAGCATTAATGTGTGGGCGCCCCACGTGGCCGATCAATATGAATTCAGCTTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgtaaaattaattaatggtacttagcttaatagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
aacttac putative branch site (score: 2)
taaaattaattaatgg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattcttgatattgaagataaagtgtgaacttaggttatttttatggtgtaaaattaattaatggtacttagcttaatagagtttaaacttacatgcagCATGCGGTGGTGTTTGTAAATGGAGAACAATACTATGGAGCTAAAGCAAGCATTAACGTGTGGGCGCCACGTGTCACTGATGCTTATGAGTTTAGTTTAT
- - - - - - - - agataaa
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaattaa