Sequence
atgc intronic sequence ATGC exonic sequence...gacttgctatctagctaggcctgaatgaatgatcagttggaaagtttgagttgagatgatatgttgaatttttgtgcatttgtttttgtttccttttcagCTAGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCGAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCC
Basic information
species | Glycine max |
transcript | GLYMA16G01660.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 3
-gacttgctatctag-ctaggcctgaatgaatgatcagttggaaagtttgagttgagatgatatgttgaattt-ttgtgcatttgtttttgtttccttttcagCTAGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCGAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCC
| || | || | || | || ||| || ||| | | | | | | || | | || |||| | ||||||||||||| || ||||| ||||||||||||||||| || ||||| |||||||| ||||||||||| || ||||| |||||||| || ||||| || || || ||||||||| | |
agcgctgaaacatattcctgggatatattgttgaacacttgaactact-aattcttgcttatttttcattttcattgttcctttgtttttgtttactc--cagCTTGAGAAAGGTGTGGATGGTTTATTTGATAGCTTTGCTAGGTTGGATTCCCGTATTTCTAGTGTTGGCCAAACAGCTGCCAAAATTGGTGATCATTTAC
upper sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 4
-------gact--tgctatctagctaggcctgaatgaatgatcagttggaaagtt---tga-gttgagatgatatgttgaatttttgtgcatttgttttt---gtttccttttcagCTAGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCGAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCC
|||| | |||| ||| | | | | || | |||| | ||| | | ||| | || ||| | || || | | || |||| || ||||||| |||||||| || ||||||| |||||||| |||||||| || |||||||||||||| ||||| || ||||| ||||| |||||| | |
gttggcagactaatactat-tagtttgattaaattccttgggtacatggatcactacctgatgaataactgacaccccgatcatttcttcaaatggtaattgaattctctttctagATAGAGAAGGGTGTGGACGGTCTGTTTGAGAGCTTTGCAAGGTTGGACGGTCGTATTTCAAGTGTTGGACAGACCGCTGCAAAAATAGGAGATCATTTGC
upper sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 3
-----gacttgctatctagctaggcctgaatgaat---gatcagttggaaagtttgagttgagatgatatgttgaatttttgtgcatttgtttttgtttccttttcagCTAGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCGAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCC
|||| |||| | | | |||| ||||| ||| ||| |||| || |||| | || | || ||||| | || | ||||||| | || |||||||| ||||| |||||||| || ||||| ||||||||||| || |||||||||||||| ||||| || ||||| || || |||||||| |
taaagtacttagaatcttga-atgtctga-tgaatctgaatctgttatgcagttcccattaagataacgc-ttcagtt-----acatttcctatttgtcttttttcagTTGGAAAAAGGTGTAGATGGTTTGTTTGATAGTTTTGCAAGGTTGGATTCCCGTATTTCAAGTGTTGGACAGACTGCTGCAAAAATTGGAGATCATCTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgagttgagatgatatgttgaatttttgtgcatttgtttttgtttccttttcagCTAGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCGAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCC
catttgtttttgtttc CT-rich tract
atatgttgaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacttgctatctagctaggcctgaatgaatgatcagttggaaagtttgagttgagatgatatgttgaatttttgtgcatttgtttttgtttccttttcagCTAGAGAAAGGTGTGGATGGATTGTTTGACAGCTTTGCGAGGTTGGATTCACGAATTTCAAGTGTTGGTCAGACAGCAGCAAAGATAGGTGATCATCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - tgctatc
- - - - - - - - -ggcctga
- - - - - - - - - - -tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtgc