Sequence
atgc intronic sequence ATGC exonic sequence...gacattatccaaatggaaataatgtagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctcttcagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33650.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 9
gacattatccaaatggaaataatg-tagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctctt-cagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
|| | | | |||| | | | |||| | || | | || | | | | || ||| | | | ||| ||| |||||||| ||||||||||| || ||||| |||||||||||||| || || || |||||||||||||| || | ||| ||| | |||||||| ||
-tcactccattgaaccacccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctatt-atataatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 9
gacattatccaaatggaaataatg-tagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctctt-cagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
|| | | | |||| | | | |||| | || | | || | | | | || ||| | | | ||| |||| |||||||| |||||||| || || ||||| |||||||||||||| || || || |||||||| ||||| || | ||| ||| | |||||||||||
-tcactccattgaaccacccaatgatcatgttcctctgttcatttcttcaatgctagctcctgagtcctatt-atataatgcaataaaattttatcttacagGAGGTGGATCCATGTGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCCACTGGACCTAAATCAGCACTGTTTGTTCCAGAA
upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 10
gacattatccaaatggaaataatgtagta-tatttctgacgttg---agctcgtggatctctgtaaatttagactgattgaattccttcacattgcctcttcagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
|| | | ||| | || | || ||||| ||| | | | || | | | | | ||| || | | || | |||||||| |||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||| || || ||||||||||||||||| |||||
---atggagaacctcacaattttttattggtaaatctgatgtttgctaatttcagagctgctatgagctcatcaagtctgaggagatttg-aatatctgtgcagGAGGTGGATCCATGTGAGGATTTGACTGATGATGACATTCGAACTGCAATTCAGAATGCAACCGGCCCTAGATCTGCATTATTTGTGCCAGAA
upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ15047 (Selaginella moellendorffii), 3'ss of exon 9
gacattatccaaatggaaataatgtagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctcttcagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
||| | | | || ||| | || | ||||| ||| ||||||||||||||||| || || |||| ||||| ||||| || || || ||||| ||||| |||||||||| | || | ||||| || ||
------------------------------------------------gtgcgttttt-tagttttg---ttatacgtccttctaacatt-tttctacagGAGGTTGATCCATGTGATGATCTGACTGATGAAGATATACGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ37641 (Selaginella moellendorffii), 3'ss of exon 9
gacattatccaaatggaaataatgtagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctcttcagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
||| | | | || ||| | || | ||||| ||| ||||||||||||||||| || || |||| ||||| ||||| || || || ||||| ||||| |||||||||| | || | ||||| || ||
------------------------------------------------gtgcgttttt-tagttttg---ttatacgtccttctaacatt-tttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcgtggatctctgtaaatttagactgattgaattccttcacattgcctcttcagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
gactgat putative branch site (score: 3)
ttgcctcttc putative PPT
tgtaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacattatccaaatggaaataatgtagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctcttcagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
- - - atccaaa
- - - - - - - -gaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - atctctg