Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttttttctagtttgtgcttttatttattcaagtatgcagcagacaagcctccgagctttcttatgttccccattttgttgattgtttgtattcctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGTAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22770.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 20
-------gtttgtttttttctagtttgtgcttttatttattcaagtatgcagcagacaagcctccgagctttcttatgt-tccccattttgttgat-tgtttgtattc--ctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGTAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
| |||||||||| | | || || || || | | | || | | | || || |||| | | | || || || | | | ||| | ||||||||||| ||||| |||||||||| || || || |||||||| ||| |||||||||||||||||||||| ||| || ||||||||| | |||
gtatttcttcattttttttctaatgttctctatttttagttttaattttggtcatgtatatttgc-agtttaaacatgtgttcttagatttttaatatatataaattgtgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 20
------gtttgtttttttctagtttgtgcttttatttattcaagtatgcagcagacaagcct-ccgagctttcttatgttcccc-attttgttgat---tgtttgtattcctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGTAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
|| |||||||||| | | || || ||| || | | | || | | | | ||| |||||| ||||| | || | | | | || | ||||||||||| ||||| |||||||||| || || || |||||||| ||| |||||||||||||||||||||| ||| || ||||||||| | |||
gtatttcttcatttttttctaatattctctattttttgttttaattttggtcatgtatatttgctgtttaaacttgtgttcctagattttatatatatatatatattttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 20
--------------------------------------------------------------------gtttgttttt-ttctagtttgtgcttttatttattcaagtatgcagcagacaagcctccgagctttct----tatgt--tccccat------tttgttga---ttgtttgt-attcctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGTAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
|| | || | || ||| || | || || | ||| ||| || | | | ||| | ||||| |||| | | ||| |||| | | ||||||||||| ||||| || ||| ||| ||| ||||| | ||||| || ||| |||||||||||||||||||| ||||| | ||||||||||||||||||
gttttaaatctttttttttaagtctttccttttgactgtaatttactctaacttaattgtcctttctggtgttttgctattatagcccacatttatgttaatactagttagca-tagttagattttttatttttttattttatgtaacttccatgagtcctatagtgaattttgtcaattaccttccagATTGGCATTAAAGCAGAGTGGCGAGCACATCATGGGCGTCTTGTCCTTTTCTTGGGAAACAAGAATACTTCTTCACTTGCTTCAGTTCAAGCTCTGATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagcctccgagctttcttatgttccccattttgttgattgtttgtattcctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGTAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
tgttgat putative branch site (score: 4)
tattcctc putative PPT
tttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttttttctagtttgtgcttttatttattcaagtatgcagcagacaagcctccgagctttcttatgttccccattttgttgattgtttgtattcctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGTAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT