Sequence
atgc intronic sequence ATGC exonic sequence...ctagtatgttgttaatatttctctcggtgggatacatgaatctattccacaccaacaaaaacatcaaaatgcttgatatttttttttcttctgttctcagATCCCTGAAGACCTCCATTTTGTGCTAAGAATGAGGCACACTTTTGAATCTCTAGGCTATCAATCAGGGTTCTACCTCTCCCAACTCTTCTCTTCAACAA
Basic information
species | Glycine max |
transcript | GLYMA06G36190.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 6
ctagtatgttgttaatatttctctcggtgggatacatgaatctat-tccacaccaacaaaaacatcaaaatgcttgatatttttttttcttctgtt-ctcagATCCCTGAAGACCTCCATTTTGTGCTAAGAATGAGGCACACTTTTGAATCTCTAGGCTATCAATCAGGGTTCTACCTCTCCCAACTCTTCTCTTCAACAA
||| || || ||||| | ||| || | || | || || | | || | || ||| || | || ||| || ||||||| |||||||| || || ||||| || | ||||||||||| |||||||| || ||||| ||||| || || |||||||| || |||||||| ||||
---gtaagtcttttttattttggttcatggt-taaaagattgtaagtcttctcttac-------ttgggatctttgcggttatgttctctaaacttactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------ctagtatgttgttaatatttctctcggtggg---atacatgaatctattccacaccaacaaaaacatcaaaatgcttgatatttttttttct-tctgttctcagATCCCTGAAGACCTCCATTTTGTGCTAAGAATGAGGCACACTTTTGAATCTCTAGGCTATCAATCAGGGTTCTACCTCTCCCAACTCTTCTCTTCAACAA
|||||| || || |||||| || | | ||| ||| || || | || | | ||| ||||| | || | | | | ||||||| || |||||||| ||||||||||| |||||| |||| || ||||||||||| || |||||||| ||||||||||||||||| |||||||||||||| |
gtgagtttcatttgtttttgtgctttgatcatctcttgtcctgctagta-attcttgatatttttcagattttgttgatatatgtatgcgtttga-gcctttgtttccttgaaaggagttgatctcattgagattatgtatgctcagATACCGGAAGACCTTCATTTTGTGCTGAGAATGCGGCATACCTTTGAATCTCTTGGGTATCAATCTGGGTTCTACCTCTCCCAGCTCTTCTCTTCAACTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccacaccaacaaaaacatcaaaatgcttgatatttttttttcttctgttctcagATCCCTGAAGACCTCCATTTTGTGCTAAGAATGAGGCACACTTTTGAATCTCTAGGCTATCAATCAGGGTTCTACCTCTCCCAACTCTTCTCTTCAACAA
gcttgat putative branch site (score: 5)
cttgatattttttttt CT-rich tract
aaaatgcttgatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagtatgttgttaatatttctctcggtgggatacatgaatctattccacaccaacaaaaacatcaaaatgcttgatatttttttttcttctgttctcagATCCCTGAAGACCTCCATTTTGTGCTAAGAATGAGGCACACTTTTGAATCTCTAGGCTATCAATCAGGGTTCTACCTCTCCCAACTCTTCTCTTCAACAA
- - - tgttgtt
- - - - - - - - - - - - cggtggg
- - - - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - ccacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttga