Sequence
atgc intronic sequence ATGC exonic sequencegtaagaataagctcaattgctttctagtggacaaagctgtattctttaattttcttagtaacgcttctttgttttgatatagGTTGAGGTTAGATTAAGAGAAGGAAAGGCAGTGAACATACACATGTTCTGTGGACGTAGACCAGGTCTTTTACTTTCCACCATGAGAGCTTTGGATAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G05390.1 (Glycine max), 3'ss of exon 2
---gtaagaataagctcaattgct-ttctagtgga---------caaagctgtattctttaattttcttagtaacgcttctttgttt-tgatat----agGTTGAGGTTAGATTAAGAGAAGGAAAGGCAGTGAACATACACATGTTCTGTGGACGTAGACCAGGTCTTTTACTTTCCACCATGAGAGCTTTGGATAACT
||| | | | ||| | | | || || | || || | |||| | ||| ||| ||||| |||||| |||||||||||||| |||| ||||| | || || ||||| || |||||||| || ||||||||||||| ||||| |||||||| ||||||||||||
ccaactagattgatttatatttttatgttgacagaatttaattgcattggtgatttgctaaattgttttaaattgactttagtgtttctgatatttatagGTTGAGGTTAGAGTAAGGGAAGGGAGAGCTGTCAACATTCATATGTTCTGCACCCGCCGACCAGGTCTTTTGCTTTCTACCATGAGGGCTTTGGATAACC
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G26290.1 (Glycine max), 3'ss of exon 2
---------------gtaagaataagctcaattgctttctagtggac---aaagctgtattcttta--attttcttagtaacgcttctttgttttgatatagGTTGAGGTTAGATTAAGAGAAGGAAAGGCAGTGAACATACACATGTTCTGTGGACGTAGACCAGGTCTTTTACTTTCCACCATGAGAGCTTTGGATAACT
|| || || | |||| || | | || | || || | | | || | | | || || ||||||| ||||||| |||| ||||| || || || || || ||||| |||| | |||||||||||||||||||| |||||||| || |||||| |
gaggaacaattagatttaggagatagtt--attggttctcacagaacttaatggcagtgcaactgaggaaattttgacttgaattttttctgaaacttatagGTGGAGGTTACGGTAAGGGAAGGGGGAGCTGTCAATATCCATATGTTTTGTGCCCACAGACCAGGTCTTTTACTTTCTACCATGAGGGCAATGGATAGCC
upper sequence: AT1G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G27480.2 (Glycine max), 3'ss of exon 2
gtaagaataagctcaat-tgctttctagtggacaaa------------gctgtattctttaattttcttagtaacgcttctttgttt-tga----tatagGTTGAGGTTAGATTAAGAGAAGGAAAGGCAGTGAACATACACATGTTCTGTGGACGTAGACCAGGTCTTTTACTTTCCACCATGAGAGCTTTGGATAACT
|| | || | || | ||| || |||| | | || || | |||| | ||| ||| ||||| ||| ||||||||||||||||| |||| ||||| | | || ||||| || |||||||| || ||||||||||||| ||||| ||||||| ||||||||||||
ttaccgactagattgatatatttttatgttgacagaatttaattgcatgttgatttgctaaattgttttaaattgactttagtgtttctgacatttatagGTTGAGGTTAGAGTAAGGGAAGGGAGAACTGTCAACATTCATATGTTCTGCACCCGCCGACCAGGTCTTTTGCTTTCTACCATGAAGGCTTTGGATAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggacaaagctgtattctttaattttcttagtaacgcttctttgttttgatatagGTTGAGGTTAGATTAAGAGAAGGAAAGGCAGTGAACATACACATGTTCTGTGGACGTAGACCAGGTCTTTTACTTTCCACCATGAGAGCTTTGGATAACT
cgcttctttgtttt CT-rich tract
tattctttaattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaataagctcaattgctttctagtggacaaagctgtattctttaattttcttagtaacgcttctttgttttgatatagGTTGAGGTTAGATTAAGAGAAGGAAAGGCAGTGAACATACACATGTTCTGTGGACGTAGACCAGGTCTTTTACTTTCCACCATGAGAGCTTTGGATAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT