Sequence
atgc intronic sequence ATGC exonic sequence...attgtaggatttatgtttcttgattgatacatacctttgatgtattttgaccagtttatttggtgttgatgctgtttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 1
-attgtaggatttatgttt---cttgattgatacatacctttgatgtattttgaccagtttatttggtgttgatgctgtttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
||||| || | || || || | || ||| | ||| | | | ||| |||| | ||| | | | | || || ||||||| ||||| ||||| ||||| || ||||||||||||||||| ||||| ||||| ||| | || |||||||| |||||||| || ||||||||||| ||
ttttgtaagacacctcttcacatttccctgtgaaatgcctgtatgctatatatttaaatatataaaatgtttaatctgatcc---actatcttgat-tgttcagGTGAAAAATTTTCTGAAATTGTGGGAAGTCCATATTACATGGCTCCTGAAGTGCTGAAGAGAAACTATGGACCTGAAATAGACATATGGAGTGCTGGTGT
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 1
--attgtaggatttatgtttcttgattgatacatacctttgatgtattttgaccagtttatttggtgttgatgctgtttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
| | ||| ||||| | || ||||| ||| | | | | | | || ||| || ||| | ||||||||| || ||||| ||||| || || |||||||||||||| || ||||| | ||| | || ||||| || |||||||||||||||||||| |||||
tggactcacagtgcttgtacaacagttgatcgttgttctt--tgtatacagacaaaactcctagttccatccagtccttatgtgattgttatgttcttttagGTGAGAAGTTTTCTGAAATTGTGGGAAGCCCATATTACATGGCTCCAGAGGTATTGAAGAGAAACTATGGTCCGGAAATAGATATTTGGAGTGCAGGAGT
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
attgtaggatttatgtttcttgattg--atacatacctttgatgtattttgaccagtttatttggtgttgatgctgt-ttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
| | || | |||| ||| | || | ||| | || | | | | | | | || ||| || || || | || |||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||
--ctcatgtttcac-tttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
-attgtaggatttatgtttcttgattg--atacatacctttgatgtattttgaccagtttatttggtgttgatgctgtttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
||| | | ||||||| ||| | || | ||| | || | | | | | | | ||| | | ||||| || | || |||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||
tgctgtct-actcatgtttcgacattatatttcaatctttttcattgcttacagtatctgacattttttccatgtgttgtgggtaata--taaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
--attgtaggatttatgtttcttgattgatacatacctttgatgtattttgaccagttt---atttggtgttgatgctgttt--ttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
||| | | || | |||| || | ||| |||| | || | | ||||| |||| | |||| || | | | | | | | | |||||||| |||||||| |||||||| ||||| ||||||||||| || ||||| || ||||||||||||||||| ||||||||||| |||||||| |||||
tagttgcaaggctt---tatcttatttaa---ataagtttgcta-atctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaccagtttatttggtgttgatgctgtttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
tgcttac putative branch site (score: 2)
tttttgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtaggatttatgtttcttgattgatacatacctttgatgtattttgaccagtttatttggtgttgatgctgtttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - acatacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tatttgg