Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgattgttgctcacctgaaattagagattcaccgtatactctccattaaatattcaaacatgtgcagGTACTGGAATTATTTGAGGAAACAAACATTTGTTTTGGAGTCATATGTAACCAAAGTTAACCAAGTAATGAACCGTGCATTATTTGCTGTTCACTGTTAT
Basic information
species | Glycine max |
transcript | GLYMA16G08510.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 10
----------------------gtttgtgattgttgctcacctgaaattagagattcaccgtatactctccattaaatattcaaacatgt-------gcagGTACTGGAATTATTTGAGGAAACAAACATTTGTTTTGGAGTCATATGTAACCAAAGTTAACCAAGTAATGAACCGTGCATTATTTGCTGTTCACTGTTAT
| || || | ||| | | | | | | | | ||||| | | |||| || ||| |||| ||||||||||| | ||||||||||| |||||| | |||||||||||| | || || ||| | |||||||||||||||||| | || || |||
atactttgggtttcttttctgtgcacatgtttat-gctaaaccaatgtatgcatcttaactaatactgttttcttcatatacatgtttgtttttcatgcagATACTGGAATTACCTCAGGAAACAAACTTTTGTTCTCGAGTCATATGTATCGAATGTAAACTGGATGATGAACCGTGCATTATTTACAAGCCATTGCTAT
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 10
gtttgtgattgttgctcacctgaaattagagattcaccgtatactctccattaaatattca-------aacatgtgcagGTACTGGAATTATTTGAGGAAACAAACATTTGTTTTGGAGTCATATGTAACCAAAGTTAACCAAGTAATGAACCGTGCATTATTTGCTGTTCACTGTTAT
|||| |||| | || | || || ||||| || || || | || || |||| || ||||||||||| |||||||| |||||||||||| | || ||||| | | || |||||| || ||||| |||||||||||| || ||||| |||
gtttttgatattcccttttcaaaatttgttttttcacatggtattccttgttgatcttttccctttttgacttgtgtagATACTGGAATTACTTGAGGAAGCAAACATTTGTTCTTGAATCATACATTTCGAAGGTTAACTGGGTTATGAATCGTGCATTATTTTCTTCCCACTGCTAT
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S194_131V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------------------gtttgtgattgttgc--tcacctgaaattagagattcaccgtat-actctccattaaatattcaaacatgtgcagGTACTGGAATTATTTGAGGAAACAAACATTTGTTTTGGAGTCATATGTAACCAAAGTTAACCAAGTAATGAACCGTGCATTATTTGCTGTTCACTGTTAT
| |||| ||| | | || | ||||| | ||| | | ||| | | ||||||||||||||||||||| |||||||||| |||| |||| | || || | ||| | |||||||| | ||| || | | || ||||
gtattattcttatgttgcctcgagcatttgcttgaatattagtgagcagtttttggctgaaagtaatggtgagcattgtggtttcttgcagttagacttcttacgtgtcgaaacttaccccttatgcttttct-tgcagGTACTGGAATTATTTGCAGAAACAAACAATTGTACTGGAAACGTACAATACAACGTATAATTACTGGATGAACCGCGGATTGTTCTTTTTGCATTGTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctgaaattagagattcaccgtatactctccattaaatattcaaacatgtgcagGTACTGGAATTATTTGAGGAAACAAACATTTGTTTTGGAGTCATATGTAACCAAAGTTAACCAAGTAATGAACCGTGCATTATTTGCTGTTCACTGTTAT
tgctcac putative branch site (score: 2)
attaaatattcaaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgattgttgctcacctgaaattagagattcaccgtatactctccattaaatattcaaacatgtgcagGTACTGGAATTATTTGAGGAAACAAACATTTGTTTTGGAGTCATATGTAACCAAAGTTAACCAAGTAATGAACCGTGCATTATTTGCTGTTCACTGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT