Sequence
atgc intronic sequence ATGC exonic sequence...accagtgaattttgaacttaattattaatcatgaatgaaattattggaccttaaatgctgatattgttatctgaattttcccctgatcctgtttttctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
Basic information
species | Glycine max |
transcript | GLYMA20G25800.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------accagtgaattttgaactt----aattattaatc--atgaatgaaattattggaccttaa-atgctgat-----attgttatc-tgaattttcccctgatcctgtttt-------tctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
| ||||||| | || ||| | || | || ||| || || || |||| | || || | | |||| | ||| || || || | | |||||| |||||||||||||||| || |||||||| |||||||||||||| ||||| ||| |||||||| || ||||| || ||||||||||||||| |
gtgtttttctcttgttggagtattactaattttatttttttcgtaacactttgaatgaatttgcattttctggaatcaatatgctaataaatatttttttttaactttaacacgcatatcatcaacttctatcatatcattttggctaattaaattgtataacaatttagAGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGTATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCC
upper sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 14
lower sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 11
accagtgaattttgaacttaattattaatcatgaatgaaattattggacct-taaatgctgatattgttatctgaattttcccctgatcctgtttttctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
| ||| || ||| |||| || | ||| | | | | ||||||| | ||| | | || ||| || |||||||||||||||| ||||| |||| ||| ||| ||||||||||||| || || | || || ||||||||||||||||| ||||||||||| |||||||
ataagtattcactgccaacaatc-ttaactatctgactggtccgtgggcttacatttagtgatatttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
upper sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
accagtgaattttgaacttaattattaatcatgaatgaaattattggaccttaaatgctgatatt-gttatctgaattttcccctgatcctgtttt---tctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
| | || || | ||| | ||| | || || | ||| || || | ||| | || || ||| | | |||||||||||||||||||| || |||||||||||| | |||||||||||||||||| ||||||| ||||||||||||||||| ||||| ||||| |||||||
-ctgattccttccaaatt---acattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaccttaaatgctgatattgttatctgaattttcccctgatcctgtttttctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
ttttcccctgatcctg CT-rich tract
atattgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accagtgaattttgaacttaattattaatcatgaatgaaattattggaccttaaatgctgatattgttatctgaattttcccctgatcctgtttttctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
- - - - - - - - - - - - - - -catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat