Sequence
atgc intronic sequence ATGC exonic sequence...gtttttttttttttttgcagttttcttaatagtgtactatttttggtgaatttaatatttactattacttatatgattatgcattgtatttgccatgtagAGTAACAATGAAAAACTGTTAGAGAACCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTGTGA
Basic information
species | Glycine max |
transcript | GLYMA18G52540.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G52540.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------------------------------------gtttttttttttttttgcagttttcttaatagtgtactatttttggtgaatttaatatttactattac--ttatatgattat--gcattgtatttgccatgt----agAGTAACAATGAAAAACTGTTAGAGAACCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTGTGA-------------
|||| | ||| || | | | ||| | ||| | | |||| | ||| | |||| | || ||| ||||| | ||| || ||||||||||||||||| | |||||||| || ||||||||| |||| ||||| || || |||| ||||| || || | | |
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
upper sequence: GLYMA18G52540.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
gtttttttttttttttgcagttttcttaatagtgtacta--tttttggtgaatttaatatttactattacttatatgattatgcattgtatt--tgccatgtagAGTAACAATGAAAAACTGTTAGAGAACCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTGTGA-------------
||||| | | ||| | ||| | | || ||| || | ||| | || || || | || | |||| || | || |||| ||||||||||| ||||||||||| || || ||||| ||| |||||||| |||| ||| |||||||||| |||| || | | |
----tttttaaagatcctaacttttgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatttaatatttactattacttatatgattatgcattgtatttgccatgtagAGTAACAATGAAAAACTGTTAGAGAACCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTGTGA
atttaat putative branch site (score: 4)
tttaatatttactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttttttttttttgcagttttcttaatagtgtactatttttggtgaatttaatatttactattacttatatgattatgcattgtatttgccatgtagAGTAACAATGAAAAACTGTTAGAGAACCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTGTGA
- - - - - - - -tgcagtt
- - - - - - - - - - - - - - - agtgtac
- - - - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcat