Sequence
atgc intronic sequence ATGC exonic sequence...ttgtcataggtttaagctaccatgtttccattgcttcaccactttattatggactagtattgttattttcttttatattaagcatttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G25720.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G29760.2 (Glycine max), 3'ss of exon 5
ttgtcataggtttaagctaccatgtttccat-tgcttcaccactttattatggactagtattgttattttcttttatattaagcatttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
|| | | |||| || | ||| | | ||| | || | || | | | | | || ||| | ||||| ||||| | ||||||| ||| ||||||||||||| ||||| ||||| || ||||||| | ||| |||||||||||||||| ||| ||||| |||| || |
--gtttttgctttaccctcctatgccccaaagtgcctgttaacatagcta--gccagatctcaaaagcttacttt----------tacaatttc--tgtagATTGGGACATTTAATCATGATATGAAAGATGGTTGGGGTCTGGCAACTGATGGAACATTGTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATTG
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G24450.1 (Glycine max), 3'ss of exon 5
ttgtcataggtttaagctaccatgtttccattgcttcaccactttattatggactagtattgttattt---tcttttatattaagcatttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
|| || | | | | | || | | | | | | | || || | | | ||| | | | ||| | |||||| | ||||||| ||| ||||||| ||||| ||||| ||||| || |||||||||| || |||||||||||||||| ||| ||||| |||| |||
ttttcctgagat---gtcatcagtgatgtgaggtgaaatccccaaagtgcctgttaacatagccacctagatctcaaacagcttacttttagaatttctgtagATTGGGACATTTAATCATGATATGAATGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATGA
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G24440.1 (Glycine max), 3'ss of exon 5
--ttgtcataggtttaagctaccatgtttccattgcttcaccactt-tattatggactagtattgttattttcttttatattaagcatttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
|||| | | | | ||| | |||| | || | ||| || | ||| | | || | ||| | ||||| ||||| || |||||||| || |||||||||| || ||||| ||||| || |||||||||| || |||||||||||||||| ||| ||||| |||| | |
ttttgtttttgttgtttcatact-tctttctgagatgctatcagtgatatgatagcgtagctagcctgatctcaaacagcttatttttacaatttc--tgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G24430.1 (Glycine max), 3'ss of exon 2
ttgtcataggtttaagctacca-tgtttccattgcttcaccactttat-tatggactagtattgttattttcttttatattaagca--tttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
|||| | || | | | | | | | | | | | || || | || | | || | |||| | |||||| || ||||||| ||| |||||||||||| ||||| ||||| || |||||||||| || |||||||||||||| | ||| ||||| |||| || |
--atcatt--cctgagatgctagcagtgatgtggggtgaatgcccaaagtgcctgttaacatagctagccagatctctaacagcttattttgcaatttctgtagATAGGGACATTTAATCATGCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatggactagtattgttattttcttttatattaagcatttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
atttgat putative branch site (score: 5)
tttcact CT-rich tract
tattgttattttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtcataggtttaagctaccatgtttccattgcttcaccactttattatggactagtattgttattttcttttatattaagcatttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG