Sequence
atgc intronic sequence ATGC exonic sequence...ctgtaatatgttccaaatgaagaacaatatttttgttttaagtttcttggtgacttatattcttttttcccttgcatatatgtaatttgtaaactggcagTATGTTGAAGTTGTTCCACAAATGGAGAAACAGAGGCGTTTGGAGCAAATCCTCAGATCCCAAGAACGGGGTTCTAAGGTCATAATATTTTGTTCCACAA
Basic information
species | Glycine max |
transcript | GLYMA15G14470.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G14470.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g46240.1 (Oryza sativa), 3'ss of exon 5
ctgtaatatgttccaaatgaagaacaatatttttgttttaagtttcttggtgacttatattctttt-----ttcccttgcata--tatgtaatttgtaaactggcagTATGTTGAAGTTGTTCCACAAATGGAGAAACAGAGGCGTTTGGAGCAAATCCTCAGATCCCAAGAACGGGGTTCTAAGGTCATAATATTTTGTTCCACAA
||| | ||| || | | | ||||| | || | || | | | ||||||| ||| || | || | | ||| ||||||||| || || ||||||| | |||| || ||| |||| |||||||| || || ||| | |||||| |||| ||||||||||| ||||| || || || |
-----gtatttatataatcaaatatagggtccttgttatgccgttttaaatggcctttcttcttttggtaattcagttctaaggttacctcctgtgtgtggatgcagTATGTAGAGGTGGTTCCACCATTGGACAAGCAGCGGCGATTGGAGCAGATACTTAGAGCTCAAGAAAGGGGCTCTAAGGTCATCATATTCTGCTCAACCA
upper sequence: GLYMA15G14470.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G06480.1 (Arabidopsis thaliana), 3'ss of exon 6
ctgtaat-atgttccaaatgaaga-acaatatttttgttttaagtttcttggtgacttatattcttttttcccttgcatatatgtaatttgtaaactggcagTATGTTGAAGTTGTTCCACAAATGGAGAAACAGAGGCGTTTGGAGCAAATCCTCAGATCCCAAGAACGGGGTTCTAAGGTCATAATATTTTGTTCCACAA
|| || || || ||| | | | | | | | || | |||| | | | || | | | | ||| ||||||||||||||| || ||||||||||||||| |||| ||||||||||||||||| || || |||||||| ||||| || || ||||||||||| ||||| |
--gtgatgatcatctaaaccattttatatcactgtaaagcaatacttacacataacttg-gtgatgaggttactgaagcaaacccatccttataac--gcagTATGTTGAAGTAGTCCCACAAATGGAGAAAGAGAGACGTTTGGAGCAAATCCTTAGGTCACAAGAACGAGGTTCAAAAGTTATAATATTTTGCTCCACGA
upper sequence: GLYMA15G14470.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g00470.t01 (Vitis vinifera), 3'ss of exon 5
ctgtaatatgttccaaatgaagaacaatatttttgttttaagtttcttggtgacttatattcttttttcccttgcata-tatgtaatttgta--aactggcagTATGTTGAAGTTGTTCCACAAATGGAGAAACAGAGGCGTTTGGAGCAAATCCTCAGATCCCAAGAACGGGGTTCTAAGGTCATAATATTTTGTTCCACAA
| ||||| | || || | | | | | | | | | | || | | | |||| || || | || | | |||| | ||| ||||||||||||||| ||| ||| | ||| || |||||||| ||||| || || || ||||||||||||||||||||||||||||| || || ||||||||||
--gaaatattctgcacattgtgcatatcactct-gcatcttctatatttgcactattttttctccaactatttacaaagtaagaattttgcatgaacctgcagTATGTTGAAGTAGTTTCACCACCGGAAAAGCAGAGGCGCTTGGAACAGATACTTAGATCCCAAGAACGGGGTTCTAAGGTCATCATCTTCTGTTCCACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtgacttatattcttttttcccttgcatatatgtaatttgtaaactggcagTATGTTGAAGTTGTTCCACAAATGGAGAAACAGAGGCGTTTGGAGCAAATCCTCAGATCCCAAGAACGGGGTTCTAAGGTCATAATATTTTGTTCCACAA
atatatgtaatttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtaatatgttccaaatgaagaacaatatttttgttttaagtttcttggtgacttatattcttttttcccttgcatatatgtaatttgtaaactggcagTATGTTGAAGTTGTTCCACAAATGGAGAAACAGAGGCGTTTGGAGCAAATCCTCAGATCCCAAGAACGGGGTTCTAAGGTCATAATATTTTGTTCCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - -cttggtg