Sequence
atgc intronic sequence ATGC exonic sequence...agctacatgtacacattaaaggatcttatgcttatttttctttccacaagggaaaacatatgtttctaattttcctccttctatttatgtgtggatttagAAATGCATACAACATGGTGCTTCACAAATTTGGGGAGAAGCTCTACTCAGGGCTGGTTGCGACCATGACTGGGCATCTCAAAGCTATAGCTCAATCTGTT
Basic information
species | Glycine max |
transcript | GLYMA08G41130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G41130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g02230.t01 (Vitis vinifera), 3'ss of exon 1
-agctacatgtacacattaaaggatcttatgcttatttttctttccacaagggaaaacatatgtttctaattttcctccttctatttatgtgtggatttagAAATGCATACAACATGGTGCTTCACAAATTTGGGGAGAAGCTCTACTCAGGGCTGGTTGCGACCATGACTGGGCATCTCAAAGCTATAGCTCAATCTGTT
| | | ||| | | | | ||||| ||| | | || | || | | | || | || || || || || ||||| ||||| ||||| || ||||||||||| |||||| | ||||||||||||||| | || |||||| |||||||||| ||| | | | | |
tactgtctctttcactctcttctctttgttcaggattttgtttttgatatcctaattttgaatcttttttacctgatgttttaacttcggtatgt-ttcagGAATGCTTACAATATGGTACTGCACAAATTTGGTGAGAAGTTGTACTCAGGGCTGGTTTCAACTATGACTTCACATCTCAAAGACATATCAAAGTTTATA
upper sequence: GLYMA08G41130.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_336V6.1 (Physcomitrella patens), 3'ss of exon 2
-agctacatgtacacattaaaggatcttatgcttatttttctttccacaagggaaaacatatgtttc-taattttcctccttctatttatgtgtggatttagAAATGCATACAACATGGTGCTTCACAAATTTGGGGAGAAGCTCTACTCAGGGCTGGTTGCGACCATGACTGGGCATCTCAAAGCTATAGCTCAATCTGTT
| | | | | || || | |||| | ||| | || | | | | | | | |||| || || || ||||| |||||||||||||| ||||| | ||| ||||| ||||||||||| | || |||| ||||| |||| | | ||||||| | ||||
catttggtgatgatctatgaaattaattgtatatattcgatacttcacgtgactaatttagtatcccatcaatcatgaattgggatttcaaaatg--ttcagGAATGCGTACAACATGGTGCTCCACAAGTATGGAGAGAAACTCTACTCAGGAGTTGTGACGACAATGACGCAGCATTTGCGGGAGATAGCTCGAATTGTT
upper sequence: GLYMA08G41130.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ05563 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------agctacatgtacacattaaaggatcttatgcttat---ttttctttccacaagggaaaacatatgtttctaattttcctc---cttctatttatgtgtggatttagAAATGCATACAACATGGTGCTTCACAAATTTGGGGAGAAGCTCTACTCAGGGCTGGTTGCGACCATGACTGGGCATCTCAAAGCTATAGCTCAATCTGTT
| ||| | || || | | | | || | ||| | ||| | | | | | | || || || | || | | || | | | ||| ||||| ||||||||||| |||||||| | ||| |||||||||||| | ||||||| | || ||||| |||| | ||| | ||| |
gttcgtgctttactttcctttgccgcgattccattccat-tccattttctttgctttgctcctcgtgaatttgcattctttagagtagatccattcttcctccttgtgctaaagtcttttttgttcttcctttctagGAATGCCTACAACATGGTTCTTCACAAGTATGGAGAGAAGCTCTACGCGGGGCTGGAAACCACGATGACGCAGCATTTGCAAGAGTTTTCTCGGGTGATC
upper sequence: GLYMA08G41130.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ26179 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------agctacatgtacacattaaaggatcttatgcttat---ttttctttccacaagggaaaacatatgtttctaattttcctcc----ttctatttatgtgtggatttagAAATGCATACAACATGGTGCTTCACAAATTTGGGGAGAAGCTCTACTCAGGGCTGGTTGCGACCATGACTGGGCATCTCAAAGCTATAGCTCAATCTGTT
| ||| | || || | | | | || | ||| | ||| | | | | | | || || || | ||| | | || | | | ||| ||||| ||||||||||| |||||||| | ||| |||||||||||| | ||||||| | || ||||| |||| | ||| | ||| |
gttcgtgctttactttcctttgccgcgattccattccat-tccattttctttgctttgctcctcgtgaatttgcattctttagagtagatccattcttcctccttgtgctctaagtcttttttcttcttcctttctagGAATGCCTACAACATGGTTCTTCACAAGTATGGAGAGAAGCTCTACGCGGGGCTGGAAACCACGATGACGCAGCATTTGCAAGAGTTTTCTCGGGTGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaagggaaaacatatgtttctaattttcctccttctatttatgtgtggatttagAAATGCATACAACATGGTGCTTCACAAATTTGGGGAGAAGCTCTACTCAGGGCTGGTTGCGACCATGACTGGGCATCTCAAAGCTATAGCTCAATCTGTT
ttctaat putative branch site (score: 2)
aaaacatatgtttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctacatgtacacattaaaggatcttatgcttatttttctttccacaagggaaaacatatgtttctaattttcctccttctatttatgtgtggatttagAAATGCATACAACATGGTGCTTCACAAATTTGGGGAGAAGCTCTACTCAGGGCTGGTTGCGACCATGACTGGGCATCTCAAAGCTATAGCTCAATCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - -catgtac
- - - - - - - - - - - - cttatgc
- - - - - - - - - - - - - - - - - - - - - -ccacaag
- - - - - - - - - - - - - - - - - - - - - - - - - ggaaaac