Sequence
atgc intronic sequence ATGC exonic sequencegtatccctgttttactcaattttctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagttattctggaacactttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43300.2 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
--------------------------------------gtatccctgttttactcaattttctcactctttcgttttgataaatgtttgtgt-aaccactcgtttgtttgcagttattctggaacactttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG
|| || || || | | || | | |||| | || | ||| || | || | || ||||||| ||||||| ||||| || || | ||||| |||||||||||||||||||| ||||| || | ||||| |||||||| | ||||| ||
gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacct-atcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG-------------------------------------------------
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 24
----------------gtatccctgttttactcaattt--tctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagttattctggaacactttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG
| || ||| || | | | ||| | ||| || | || | | |||| | | ||| |||| || | ||||||||||| || || | || ||||| ||||||||||| || |||||||| |||||||||||||| || ||| ||||| | || || ||
gtaagaataattttctttgtctttgtctttgttattgcagtctaagtctactattgcatttgtggtgtatctaacacatggacattttacagTCATCTTAGAACACTTTGATCAAGTAGTGGGAGACTGTTTCATGGATTGCGTGAATTGTCTGATCAGGTTTGCCAACAATAAAACTTCACATCGTATTAG-------------------------------------------------
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 24
--------------gtatccctgttttact-caattt---tctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagttattctggaacactttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG
| | |||| | | | || | | ||| | ||| || | || | | |||| | | ||| |||| || | ||||||||||| || || | || ||||| ||||||||||| || |||||||| |||||||||||||| || ||| |||| | || || ||
gtaagaataattttctttgtctgtgtcattgcagtctaagtctaagtctactattgcatttgtggtgtatctaacgcatggacattttacagTCATCTTAGAACACTTTGATCAAGTAGTGGGAGACTGTTTCATGGATTGCGTGAATTGTCTGATCAGGTTTGCCAACAATAAAACTTCGCATCGTATTAG-------------------------------------------------
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 24
-------------------------------gtatccctgttt-tactcaattttctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagttattctggaacactttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG
|| | | || | |||||| || || ||| || | || | |||| || | ||||||||||| |||| |||||||| ||||| | || |||||||| ||||| |||||||| |||||||| | ||| ||||||| ||| ||| | || || ||
gtaagaacatgccatttttcttctttcttatgtgtttttacttattctcaatgttttcttctttttgtcatttctgatac--atttaacacgaagtatatttgcagTTATCTTGGAGCACTTTGATCAGGTAGTTGGAGACTGCTTTATGGACTGTGTCAACTGTCTCATTGGCTTTTCCAATAATAAAAGTTCCCATCGCATCAG------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG
ctttgac putative branch site (score: 4)
ttgtctc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccctgttttactcaattttctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagttattctggaacactttgaccaggtgataggtgactgcttcatggattgtgtcaattgtctcatcagGTTTGCCAATAACAAAGCTTCAGACCGGATAAGCCTGAAAGCTATTGCCCTTCTCAGAATATGTGAGGATCGGCTTGCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT