Sequence
atgc intronic sequence ATGC exonic sequence...ctagttatttttctttttttgtctgagaagatagagatgaattttgtttgtgttgctgtactttttggttgtcttttagtgagatgagtaatgtgcgcagGTTTAAAGCTAATGAAATGTTGGAGATGCTAAGAGGGAAACGTTTAGTTTTTGTTGGTGATTCCCTCAATAGGAATATGTGGGAATCTCTGGTTTGTGTT
Basic information
species | Glycine max |
transcript | GLYMA20G38730.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38730.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g10560.1 (Oryza sativa), 3'ss of exon 1
-ctagttatttttctttttttgtctgagaagatagagatgaattttgtttgtgttgctgtactttttggttgtcttttagtgagatgagtaatgtgcgcagGTTTAAAGCTAATGAAATGTTGGAGATGCTAAGAGGGAAACGTTTAGTTTTTGTTGGTGATTCCCTCAATAGGAATATGTGGGAATCTCTGGTTTGTGTT
|| | || | | | || | |||||||| || | || | | || || | | | || | | | || || || | | ||| |||||||||| ||| || |||||| | | ||||| ||||||||||| || |||||||| ||||||||||| ||||| || |
gtgaggaaaagttactagagcaggcaatca-attttggtgaatttttattccatcttagtgcataaca--tgcct---aattatattcttgttatat-tagATTGAATCCAACTGATATGTTGGAGAGGCTGAGGGGGAAAAGACTGGTTTTCGTTGGTGATTCACTTAATAGGAACATGTGGGAATCCCTGGTCTGCATC
upper sequence: GLYMA20G38730.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g53380.1 (Oryza sativa), 3'ss of exon 1
ctagttatttttctttttttgtctgagaagatagagatgaattttgtttgtgttgctgtactttttggttgtcttttagtgagatgagtaatgtgc---gcagGTTTAAAGCTAATGAAATGTTGGAGATGCTAAGAGGGAAACGTTTAGTTTTTGTTGGTGATTCCCTCAATAGGAATATGTGGGAATCTCTGGTTTGTGTT
| | | |||| | | | | ||| ||| || || | | | | | | || | | |||| | ||| || || | | ||| |||||||||| ||| || ||||| | | || ||||| |||||||| ||||| ||||| ||||||||||| |||||||| |
-------gtgagttgagactacttgagcaactct-gttttattcagttcttggtgtttcatgtgaca-cagctgaaaattcagttccatgatgttcataacagATTGAACCCGAGTGACATGTTGGAGAGGCTGAGGGGGAAGAGGCTGGTGTTTGTCGGTGATTCGCTCAACAGGAACATGTGGGAATCCCTGGTTTGCATC
upper sequence: GLYMA20G38730.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G033805_T01 (Zea mays), 3'ss of exon 1
ctagttatttttctttttttgtctgagaagatagagatgaattttgtttgtgttgctgtactttttggttgtcttttagtgagatgagtaatgtg----cgcagGTTTAAAGCTAATGAAATGTTGGAGATGCTAAGAGGGAAACGTTTAGTTTTTGTTGGTGATTCCCTCAATAGGAATATGTGGGAATCTCTGGTTTGTGTT
|| | | || || ||| | | ||| |||| || | | | | | || | |||| ||| || | | |||| ||| || || | | || |||||||||| ||| ||||| ||| | | || || ||||||||||| ||||||||||| ||||||||||| || || ||| ||
---gtgaggataaggttactg-----gaacaatgcaatgg-ttttaattatttcatttcaatcttggtttgtaatttgtcaagttcatgtttgtgtcatttcagATTGAACCCAACCGATATGTTGGAGAGGCTGAGAGGAAAAAGACTGGTGTTCGTTGGTGATTCGCTCAATAGGAACATGTGGGAATCCCTTGTGTGTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtgttgctgtactttttggttgtcttttagtgagatgagtaatgtgcgcagGTTTAAAGCTAATGAAATGTTGGAGATGCTAAGAGGGAAACGTTTAGTTTTTGTTGGTGATTCCCTCAATAGGAATATGTGGGAATCTCTGGTTTGTGTT
tacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagttatttttctttttttgtctgagaagatagagatgaattttgtttgtgttgctgtactttttggttgtcttttagtgagatgagtaatgtgcgcagGTTTAAAGCTAATGAAATGTTGGAGATGCTAAGAGGGAAACGTTTAGTTTTTGTTGGTGATTCCCTCAATAGGAATATGTGGGAATCTCTGGTTTGTGTT
- - - - - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - tgttgct