Sequence
atgc intronic sequence ATGC exonic sequence...tggtagtggatcaatcatcatgctctacaaacattttcatcatggctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17150.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G048582_T01 (Zea mays), 3'ss of exon 3
---tggtagtggatcaatcatc-atgctctacaaacattttcatcatggctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
| | ||| |||| | ||| ||| ||| | || || | || ||||| | | | | || ||| || | | | |||| ||||| || ||| | ||||| ||||||||||||||||| |||| || ||||| || ||||| ||||||||||| | || || | | || |||||
tccagattgtgatagaatcttttatgacagacag-catgcttat-atatcgtttgatctggttgcaaacttgcaaatatacttacttt--tttatctctcccagTGTGTCCCACGACCCTCAAAAGAATATGCAGGCAACATGGTATAACCCGCTGGCCATCACGAAAGATCAAGAAGGTAGACCACTCTCTAAGAAAGCTCCA
upper sequence: AT2G17150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G48080.1 (Glycine max), 3'ss of exon 1
tggtagtggatcaatcatcatgctctacaaacattttcatcatg-gctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
| | || || || || || || ||| || | | | | ||| | | | | || | ||||| ||||| || || |||||||||||||||| |||||||| |||| ||||||||| || | ||||| |||||||| ||||| || ||||||||||| ||
----------------gtgagatattattaat-ttgatatgatccattaattaattgcattcctcatgtagctcttaatgaatgaattgcatgcat-gcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
upper sequence: AT2G17150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
------tggtagtggatcaatcatcatgctctacaaacattttcatcatggctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
| | |||| ||| | || |||| ||| | ||| | || | || || ||||| ||| |||||||| || || |||||| ||||||||||||||||||||||||| || | || ||||| ||||| || |||||||| ||||| || || || | |||||||||
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgttt--ccagctcactaccaattg-cttacctggtttgtttcg---gttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
atctgac putative branch site (score: 3)
tttcgttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtagtggatcaatcatcatgctctacaaacattttcatcatggctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - -atcaatc
- - - - - - - - - -atgctct
- - - - - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttcg