Sequence
atgc intronic sequence ATGC exonic sequence...atttaggggggtaatggggtgtcatatatgataaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttcttatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTCCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACACCGAGCCTGTCCTC
Basic information
species | Glycine max |
transcript | GLYMA14G23860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G23860.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 4
atttaggggggtaatggggtgtcatatatgataaaagatagacatactcataagct---aaatgcaaattc-tcata-aatgtgttactccttttcttatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTCCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACACCGAGCCTGTCCTC
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--------------------gtaacgca--atgaatgattcaggcatttacaatgtccggagtaccagttaatgatatgttttgatgtggtctgtgtgttctcagGTACCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTCAGAACACATGTGCTCACAGAGCCTGCCCTC
upper sequence: GLYMA14G23860.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
atttaggggggtaatggggtgtcatatatgataaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttcttatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTCCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACACCGAGCCTGTCCTC
|| || | | ||| || | | | || | | | || | | ||| | | || || | || |||||| | |||||||| ||||||||||| | ||||| || |||||||| || ||||||| ||||||||||| |||||| ||||| ||| |||| || ||||
--gtaaaaacaacgtgcgat-tcaggcatttttttacgaggtcagagttagcagttgcag--aaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
upper sequence: GLYMA14G23860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------atttaggggggtaat--ggggtgtcatatatgataaaagatagacatactcataagctaaatgcaaattctcata--aatgtgttactccttttcttatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTCCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACACCGAGCCTGTCCTC
| | | | ||| | | | | | | | || | | | | || | || || | || || | |||||| | | |||||| ||||| || || ||||||||||| |||||| |||| || ||| |||||||||| ||||||||||| | |||||||| || || |||| || ||||
gtaagccagttttccaaacatctaaggctcatatttagtgattaaatacagattttccacattgtggctactcaacaatgtcttaagtagcaataagagaggaggcaaacatttatagcttatctggccttgtgataatctgtgagttttccttgtaacagttttcacctttttctgtttcagATTCCAATTGATTGCTTTGAGGAACCGTGGGTTGTCTTTCGTGGGCAAGATGGGAAACCTGGATGTGTCCGTAACACCTGCGCCCATAGAGCATGCCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcataagctaaatgcaaattctcataaatgtgttactccttttcttatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTCCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACACCGAGCCTGTCCTC
agctaaa putative branch site (score: 3)
tgttactccttttctt putative PPT
aaattctcataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttaggggggtaatggggtgtcatatatgataaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttcttatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTCCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACACCGAGCCTGTCCTC
- - -ggggggt
- - - - - - - tggggtg
- - - - - - - - - - - - - - - - aaaagata
- - - - - - - - - - - - - - - - - - - - - catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa