Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgcaaattgttatgattatttctagcctctttaatgaacaacattcatcttaaaccaaagttttctgattttgtttttctagGTACTTGCACGAAGTTTGCTTGCCTTCAATTGTCCATAGAAACTTCAAATCAGCGAATATATTGCTAGACGAAGAACTTAATCCTCACCTATCAGACAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22130.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G11820.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------------------gtatgtgcaaattgttatgattatttctagcctctttaatgaac-aacat-tcatcttaaaccaaagttttctgattttgtttt-tcta---gGTACTTGCACGAAGTTTGCTTGCCTTCAATTGTCCATAGAAACTTCAAATCAGCGAATATATTGCTAGACGAAGAACTTAATCCTCACCTATCAGACAGT
| | | ||| || ||| | | | | ||| | ||| ||| || | | || || || || || ||| |||| ||||| |||| ||||| ||||||||||| |||| |||||||| |||||||| || |||||||| || || || || || ||||||||||| || ||| |
gtatgttacattcacatatctgacatattaagtctctccttggcatggccttgactggctactccacccccctgcttttccctcaagtatatttgttttagccttgtagagtgagttagcatgtcacattcaggctaatttctcaagttatgctttgtctatcagGTACCTGCATGAAGTGTGCTTGCCTTCTGTTGTACATAGAAATTTCAAATCTGCAAATATATTACTCGATGAGGAGCTCAATCCTCACCTGTCTGACTGC
upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G00970.1 (Glycine max), 3'ss of exon 12
-------------------------------------------------gtatgtgcaaattgttatgattatttctagcctcttta--atgaac-aacat-tcatcttaaaccaaagttttctgattttgtttttc----tagGTACTTGCACGAAGTTTGCTTGCCTTCAATTGTCCATAGAAACTTCAAATCAGCGAATATATTGCTAGACGAAGAACTTAATCCTCACCTATCAGACAGT
| || | | | ||| | | || ||| | ||| ||| || | | || || | || || ||| |||||| |||| ||||| ||||||||||| |||| |||||||| |||||||| || |||||||| || || || || || ||||||||||| || ||| ||
gtatgtttcattcacatctgacatattaagtctctctttggcatggccttgactggctacccgacccccctgtttttccctcaagtagagtgagttagcatatcacattcaggctaatttcttgagttatgctttgtatgtcagGTACCTGCATGAAGTGTGCTTGCCTTCTGTTGTACATAGAAATTTCAAATCTGCAAATATATTACTTGATGAGGAGCTCAATCCTCACCTGTCTGACTGT
upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 12
gtatgt-gcaaattgttatgattatttctagcctctttaatgaaca-acattcatcttaaaccaaagttttctgattttgtttttctagGTACTTGCACGAAGTTTGCTTGCCTTCAATTGTCCATAGAAACTTCAAATCAGCGAATATATTGCTAGACGAAGAACTTAATCCTCACCTATCAGACAGT
|||||| || || || | || |||| | || ||| || ||||| || | | || | ||||| ||||| ||||||||| ||||||| | ||| ||||||||||||||||| || ||||| ||||| || ||||| || || || || |||||||| ||
gtatgttacatgttctttaagtctctttctctctctctctctctcacacacacacactaaactgtagctcc------tgcttctctcagGTATTTGCATGAAGTTTGCCTGCCTTCTACTGTACATAGAAACTTCAAATCGGCAAATATTTTGCTTGATGAAGAGCTCAACCCCCATTTATCAGACTGT
upper sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s2594g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtatgt-gcaaattgtt-atgattatttctagcctctttaatgaacaacattcatcttaaaccaaagttttctgattttgtttttctagGTACTTGCACGAAGTTTGCTTGCCTTCAATTGTCCATAGAAACTTCAAATCAGCGAATATATTGCTAGACGAAGAACTTAATCCTCACCTATCAGACAGT
|||||| || || || | | | ||||| | | | || || ||||| || | | || | ||||| ||||| ||||||||| ||||||| | ||| ||||||||||||||||| || ||||| ||||| || ||||| || || || || |||| ||| ||
gtatgttacatgttctttaagtctctttctctctctctctctctctctcacacacactaaactgtagctcc------tgcttctctcagGTATTTGCATGAAGTTTGCCTGCCTTCTACTGTACATAGAAACTTCAAATCGGCAAATATTTTGCTTGATGAAGAGCTCAACCCCCATTTATCGGACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttaatgaacaacattcatcttaaaccaaagttttctgattttgtttttctagGTACTTGCACGAAGTTTGCTTGCCTTCAATTGTCCATAGAAACTTCAAATCAGCGAATATATTGCTAGACGAAGAACTTAATCCTCACCTATCAGACAGT
ttctgat putative branch site (score: 3)
ttttgtttttct CT-rich tract
attttgtttttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgcaaattgttatgattatttctagcctctttaatgaacaacattcatcttaaaccaaagttttctgattttgtttttctagGTACTTGCACGAAGTTTGCTTGCCTTCAATTGTCCATAGAAACTTCAAATCAGCGAATATATTGCTAGACGAAGAACTTAATCCTCACCTATCAGACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC