Sequence
atgc intronic sequence ATGC exonic sequencegtttggtgtatattaggattgtcaatttgtctcagtgtcatgtaagcaatattctcatctgatgtaatctaataaaactctgctgtatattgcagGCGTCCGTGGAACTTCAAGGCATCAAAGGAATGTGGTCGTTGAAATCGTCAATTGATGAAGCCTTTGATACATTCCTTGTAGTTAGTTTTATCAGTGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21100.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 12
--------------------------------------------------gtttggtgtatattaggattgtcaatttgtctcagtgtcatgtaagcaatattctcatctgatgtaatctaataaaactctgctgtatattgcagGCGTCCGTGGAACTTCAAGGCATCAAAGGAATGTGGTCGTTGAAATCGTCAATTGATGAAGCCTTTGATACATTCCTTGTAGTTAGTTTTATCAGTGAAA
|| || |||| || | || | | | ||| | || | || | | | | | || | | | | |||| || || ||||||||||| ||||||||||||||||| ||| ||| |||| ||||| | |||||||| || || || || |||||||| |||||||
gtcagctccccttcctctacctcagtgtggaatatttgcacccaagacacattcaaaaggaatggaaattggaaaaataaatctttatattaatgacaaactccttacaaaatattaatttttttatgcatg-tatttgatctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTGAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 12
--------------------------------------------------gtttggtgtatattaggattgtcaatttgtctcagtgtcatgtaagcaatattctcatctgatgtaatctaataaaactctgctgtatattgcagGCGTCCGTGGAACTTCAAGGCATCAAAGGAATGTGGTCGTTGAAATCGTCAATTGATGAAGCCTTTGATACATTCCTTGTAGTTAGTTTTATCAGTGAAA
|| || |||| || || | | ||| || | || | | | | | || | | | | |||| || || ||||||||||| ||||||||||||||||| | | ||| |||| ||||| | |||||||| || || || || |||||||| |||||||
gtcagctccccttcctccaccacagtgtggaacatttgctcccaagactcattcaaaaggaatggaaattggaaaaacaaatctttatatcaatggcacacaccttacaaaatattaatttttttatgcatg-tatttggtctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTTAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
upper sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 12
gtttggtgtatattag--gattgtcaatttgtctc---agtgtcatgtaagca---atattctcatctgatgtaatctaataaaactctgctgt-atattgcagGCGTCCGTGGAACTTCAAGGCATCAAAGGAATGTGGTCGTTGAAATCGTCAATTGATGAAGCCTTTGATACATTCCTTGTAGTTAGTTTTATCAGTGAAA
|| ||| ||| | | || ||| |||| | | | | | || ||| || ||| | | || ||| | || || |||| || |||||||||||||||||||||||||||||||| |||| ||| || | |||||| | ||| || ||| | || || || ||||||||||| |
gtctggcttatttcaaccattttcttattgatctctagaatttgactttgccatttataagttcttctaaacttgcttattaatgtgcatatgccatcacatagGCATCAGTGGAACTTCAAGGCATCAAAGGAATGTGGTCATTGAGATCTTCTACTGATGATCCACATGACACCTTCTTGGTTGTAAGCTTTATCAGTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaagcaatattctcatctgatgtaatctaataaaactctgctgtatattgcagGCGTCCGTGGAACTTCAAGGCATCAAAGGAATGTGGTCGTTGAAATCGTCAATTGATGAAGCCTTTGATACATTCCTTGTAGTTAGTTTTATCAGTGAAA
atctaat putative branch site (score: 3)
atgtaatctaataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggtgtatattaggattgtcaatttgtctcagtgtcatgtaagcaatattctcatctgatgtaatctaataaaactctgctgtatattgcagGCGTCCGTGGAACTTCAAGGCATCAAAGGAATGTGGTCGTTGAAATCGTCAATTGATGAAGCCTTTGATACATTCCTTGTAGTTAGTTTTATCAGTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC