Sequence
atgc intronic sequence ATGC exonic sequencegtatgtataagcatggcgcttttcattctctcttattcttatttgatttcaaatagtttaaactctctttcgtttgtgatcagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTTGCCTTAGCCAAGAAGGAGGACCATGTGCCATTCAGAAACTCAAAGCTTACATATCTGC
Basic information
species | Glycine max |
transcript | GLYMA06G41600.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgtataagcatggcgcttttcattctctcttattcttatttgatttcaaatagtttaaactctctttcgtttgtgatcagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTTGCCTTAGCCAAGAAGGAGGACCATGTGCCATTCAGAAACTCAAAGCTTACATATCTGC
||| || | | | ||| | ||||| |||| | | ||||||| || ||| || ||||||||||||||||||||| || || || | ||||| ||||| |||||||| ||||| || || ||||| |||||| ||||||||||||| |||||||| |
gtacgtttgatagaaacataaaacatgattatggtttcttgc--aatttttagtctcttaaactttcattctttct---tcagGCAATCAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTC
upper sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 15
gta-tgtataagcatggcgcttttcattctctcttattcttatttgatttcaaat-agtttaa--actctctttcgtttgtgatcagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTTGCCTTAGCCAAGAAGGAGGACCATGTGCCATTCAGAAACTCAAAGCTTACATATCTGC
||| ||| | | || | || | | | | | ||||| | || | |||| | | |||| || |||||||||||||||| ||||| || || | ||||| |||||||||||||| ||||| || || || || || ||||||||||||||||| || ||||| |
gtaatgtctgcgaatcttagtaaacacatttttagagacacaagagatttaatattggcttaatgattttcttcttcttactgaaagGCAATCAACAAAAGCTTATCGTCTCTAGGCGATGTCATATTTGCCTTAGCGAAGAAAGAAGATCACGTTCCTTTCAGAAACTCAAAGCTCACTTATCTTC
upper sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 14
-------------gtatgtataagcatggcgcttttcattctctcttattcttatttgatttcaaatagtttaaactctctttcgtttgtgatcagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTTGCCTTAGCCAAGAAGGAGGACCATGTGCCATTCAGAAACTCAAAGCTTACATATCTGC
|| |||| | || || ||| | ||||| |||| || | || | | | |||| || ||| ||||| ||||| || ||| | |||||| | |||||||||||||||||| | || ||||||||||||||||| ||||| || |||||||||||||| ||||| |
gtatttgagaaacactgatacaagcttaattctgttaatttta-cttatcattatgcatctttatatttatatatattcttttcaattatga-cagGCCATCAATAAGAGTCTGTCATCATTAAGTGATGTTATATTTGCCCTGGCAAAGAAGGAGGACCATGTACCATTTAGGAACTCAAAGCTTACGTATCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcttattcttatttgatttcaaatagtttaaactctctttcgtttgtgatcagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTTGCCTTAGCCAAGAAGGAGGACCATGTGCCATTCAGAAACTCAAAGCTTACATATCTGC
atttgat putative branch site (score: 5)
ctctctttcgtttgt putative PPT
tattcttatttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtataagcatggcgcttttcattctctcttattcttatttgatttcaaatagtttaaactctctttcgtttgtgatcagGCAATCAACAAAAGTTTATCATCACTGAGTGATGTTATATTTGCCTTAGCCAAGAAGGAGGACCATGTGCCATTCAGAAACTCAAAGCTTACATATCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA