Sequence
atgc intronic sequence ATGC exonic sequencegttcgtcttctcattgagtcatttccataaacttgattcaattcttggtttaaacactcagattttgataaaggagaatgtggaatttgtgtgtatagTGCTGGAACTGGGTTGCTATCAATGATGGCTGTGAGAGCAATGAGAGGTGATTCAAAAGGAATGGTGACGGCGTGTGAGTCTTACTTACCGATGGTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16570.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G04600.1 (Glycine max), 3'ss of exon 1
gttcgtcttc-tcattgagtcatttccataaacttgattcaattcttggtttaaacactcagattttgataaaggagaatgtggaa-tttgtgtgtatagTGCTGGAACTGGGTTGCTATCAATGATGGCTGTGAGAGCAATGAGAGGTGATTCAAAAGGAATGGTGACGGCGTGTGAGTCTTACTTACCGATGGTTAAG------
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gtactccaagatcattt--taatttttaatttttttaataaaaaaatggcttcattgtgcagtttttgtataatgcgattctacttcttcaattgtgtagTGCTGGAACTGGGTTGCTTTCGATGATGGCTGCACGTGCCATGGGTGATGA------AGGGAGGGTCACGGCGTGTGAGTCTTACCTTCCAATGGTGAAGCTGATG
upper sequence: AT4G16570.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0154g00540.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------gttcgtcttctcattgagtcatttccat---aaacttgattcaattct-tggtttaaacactcagattt---tgataaaggagaatgtggaatttgtgt-gtatagTGCTGGAACTGGGTTGCTATCAATGATGGCTGTGAGAGCAATGAGA---GGTGATTCAAAAG-GAATGGTGACGGCGTGTGAGTCTTACTTACCGATGGTTAAG
|| | ||||||| | ||| ||| | ||| | | | || || | | | ||| | || || | |||| | | || |||||||||||||| ||| ||||||||||||||| || |||||| | ||||| ||| | | | | | | || | || | ||
gtacctcttatatactttgcataatcctgtgtgtggtttgtctcattagattattgacattggagactctgcccttctgggtaattgaatctgtgtggtttctttcttattggtcgcaattcaattattattgtgcagTGCTGGAACTGGCTTGTTATCAATGATGGCTGCAAGGGCAATGGGCTCTGGTGACTCAGTGGCGTGTCCTAGAACTGAGGGAATGGTAACAGCATGTGAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtttaaacactcagattttgataaaggagaatgtggaatttgtgtgtatagTGCTGGAACTGGGTTGCTATCAATGATGGCTGTGAGAGCAATGAGAGGTGATTCAAAAGGAATGGTGACGGCGTGTGAGTCTTACTTACCGATGGTTAAG
ttttgat putative branch site (score: 4)
attttgataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtcttctcattgagtcatttccataaacttgattcaattcttggtttaaacactcagattttgataaaggagaatgtggaatttgtgtgtatagTGCTGGAACTGGGTTGCTATCAATGATGGCTGTGAGAGCAATGAGAGGTGATTCAAAAGGAATGGTGACGGCGTGTGAGTCTTACTTACCGATGGTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA