Sequence
atgc intronic sequence ATGC exonic sequencegttggaaatgcatactttccactttttgattattgtttgcattgtaatgtataatatcttttatgttgtagTTTCCGAAACTTTGCGGGATGACGGGTACAGCATCGACCGAGAGTGCAGAATTTGAAAGCATATACAAGCTTAAAGTTACAATTGTACCCACAAATAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01800.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G01060.3 (Glycine max), 3'ss of exon 8
--------------------gttggaaatgcatactttccactttttgattattgtttgcattgtaatgta---taatatcttt----tatgt-----tgtagTTTCCGAAACTTTGCGGGATGACGGGTACAGCATCGACCGAGAGTGCAGAATTTGAAAGCATATACAAGCTTAAAGTTACAATTGTACCCACAAATAAGC
| || | | || || ||| || | | ||||| || || || | || | || |||| | ||||| || |||||||| || ||||| || || ||| | || || ||| |||||||||| ||||| ||||||||||||||||||||||| || ||||| || |
gttggaaatgttgtatctgagctgattaagtgaaccatca--tttcagaatttcatttgcctttgaacttaccttgatgttttcaaaccatgtacctctatagTTCCCCAAACTTTGTGGTATGACTGGCACTGCAGCAACAGAAAGTACAGAATTTGAGAGCATTTACAAGCTTAAAGTTACAATTGTGCCAACAAACAAAC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 8
--------------------gttgg-aaatgcat--actttccactttttgattattgtttgcattgtaatgtataatatcttttatgt-----tgtagTTTCCGAAACTTTGCGGGATGACGGGTACAGCATCGACCGAGAGTGCAGAATTTGAAAGCATATACAAGCTTAAAGTTACAATTGTACCCACAAATAAGC
| || || || || | || || ||| ||| |||| | | | || | || |||| | |||| || |||||||| || ||||| || || ||| | || || || |||||||||| ||||| ||||| ||||||||||||||||| || ||||| || |
gttggaaatgttgtatctgagctgataagtgaatcatcatttcagaatttcatttgcctttgaacttaccttgatgctttcaaccatgtacctctacagTTCCCCAAACTTTGTGGTATGACTGGCACTGCAGCAACAGAAAGCACAGAATTTGAGAGCATTTACAAACTTAAAGTTACAATTGTGCCAACAAACAAAC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------gttggaaatgcatactttc-cactttttgattattgttt-gcattgtaatgtataatatctttta--tgttgtagTTTCCGAAACTTTGCGGGATGACGGGTACAGCATCGACCGAGAGTGCAGAATTTGAAAGCATATACAAGCTTAAAGTTACAATTGTACCCACAAATAAGC
|| | |||| || | || | || | | || || || ||| |||| ||| || ||||| ||||||| || ||||| || ||||| || || ||| | || || | |||||||| | ||||||||||||||||||||||||||||| |||||||| || |
gttggaacatcttatttcccaaatcatttcatgaagcatgtttggatatttactttccatcttctagctttctagtgt-taatttctattcactgttgcagTTTCCAAAGCTTTGTGGAATGACTGGCACCGCAGCAACTGAAGGCACAGAATTTCAGAGCATATACAAGCTTAAAGTTACAATTGTGCCCACAAACAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccactttttgattattgtttgcattgtaatgtataatatcttttatgttgtagTTTCCGAAACTTTGCGGGATGACGGGTACAGCATCGACCGAGAGTGCAGAATTTGAAAGCATATACAAGCTTAAAGTTACAATTGTACCCACAAATAAGC
ttttgat putative branch site (score: 4)
tatctttt putative PPT
attgtaatgtataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggaaatgcatactttccactttttgattattgtttgcattgtaatgtataatatcttttatgttgtagTTTCCGAAACTTTGCGGGATGACGGGTACAGCATCGACCGAGAGTGCAGAATTTGAAAGCATATACAAGCTTAAAGTTACAATTGTACCCACAAATAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT