Sequence
atgc intronic sequence ATGC exonic sequence...aagacaagaaaccaacatcacatgcatgtcccataataatcttacctcctgcaacaattcattggggtgtgagtgtgaatattgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTTGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
Basic information
species | Glycine max |
transcript | GLYMA12G03490.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
aagacaagaaaccaacatcacatgcatgtcccataataatcttacctcctgcaaca--attcattggggtgtgagtgtgaatattgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTTGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
| | | | || | | ||| | ||| | || | || || | || || | | | | || ||||||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| || || ||||| || || || || || || || || || ||||||
-------gtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 3
aagacaagaaaccaacatcacatgcatgtcccataataatcttacctcctgcaacaattcattggggtgtgagtg--tgaatattgttttaatgt--tgtt-cagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTTGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
| | | ||| ||| | || | | || | | | | |||| | ||| | | ||||| |||| |||||||||||||||||||||||| || |||||||||||||| ||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||| ||||||
-----------------------gtactttatataccaattctttcttcaggaaaatgagactaatgatgtagtggtttaatggtaagtgaatgtgttgttgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACATACATATTTGGAGCATGTTGTGCAACCACAGTCTTTATTCCTTCCTTCCACAAC
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------aagacaagaaaccaacatcacatgcatgtcccataataatcttacctcctgcaacaattcattggggtgtgag------tgtgaatattgttttaatgtt-gtt-cagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTTGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
| | | | || ||| | | | || ||| ||||| | | | |||| | || | | | | ||| ||| |||||||||||||||||||||||| || |||||||||||||| |||||||||||||| ||||| |||||||||||||| |||||||||||||| || ||||||
gcatctccctctctccctccctatcctcctcctactactactctctctctctctctctctctttctctgtctcttgttttttcttcacccaccacatttttttttcctttctttacaataaacaaagatctgaggcattttctgcaactgggcatgtcgtttgttgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACTTACATCTTCGGAGCCTGCTGTGCCACCACAGTCTTTATTCCTTCATTCCACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcctgcaacaattcattggggtgtgagtgtgaatattgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTTGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
ttttaat putative branch site (score: 3)
aatattgttttaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagacaagaaaccaacatcacatgcatgtcccataataatcttacctcctgcaacaattcattggggtgtgagtgtgaatattgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTTGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- -acaagaaa
- - - - - -ccaacat
- - - - - - - - - - - - catgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - caattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgtga