Sequence
atgc intronic sequence ATGC exonic sequence...gactctaatttatttagtgtattattgttatgtgattttgatcttgtaatgtactttggtggttgtttcattcaataagccaaactagtctctattgtagGAATTAAGATTGATGATGAAGAACTCGCCCGTTTTGTTGAGCGTGTTGATAAGGATAATAATGGTGTTATAACATTTGAAGAATGGAGGGATTTTCTGCT
Basic information
species | Glycine max |
transcript | GLYMA16G05100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g10740.1 (Oryza sativa), 3'ss of exon 1
gactctaatttatttagtgtattattgttatgtgattttgatcttgtaatgtactt-----tggtggttgttt---cattcaataagccaaactagtct-ctatt-gtagGAATTAAGATTGATGATGAAGAACTCGCCCGTTTTGTTGAGCGTGTTGATAAGGATAATAATGGTGTTATAACATTTGAAGAATGGAGGGATTTTCTGCT
||| | |||| ||| | | | || || | || | || | | || || ||| | | ||| | | ||| | || || | ||| || | |||||||| || || || || | |||||||||| ||| ||||||||||||||||| |||| || ||||||||||||||||| ||||| |
----------ggtttttttccctattattaaatcactatgtcctaggaaagcacctgataattgtagtccttttgatgtcttacaagtaatatcagtttgctgtttgcagGCATAGAAATTGATGACGAGGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGATAATAATGGAATTATTACTTTTGAAGAATGGAGGGACTTTCTTTT
upper sequence: GLYMA16G05100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G041831_T06 (Zea mays), 3'ss of exon 2
gactctaatttatttagtgtattattgttatgtgattttgatcttgtaatgtactttggtggttgtttcattcaataagccaaactagtct-ctat-tgtagGAATTAAGATTGATGATGAAGAACTCGCCCGTTTTGTTGAGCGTGTTGATAAGGATAATAATGGTGTTATAACATTTGAAGAATGGAGGGATTTTCTGCT
| || | | | || | || | | || |||| | ||| | | || | | | || | |||| | ||| | || | || ||| || ||||| |||||||||| || || | |||||||||| ||| |||||||| || ||||| |||| || |||||||||||||| |||||||| ||
-gatatactcttctatgtct-ttgtgaccaggttatttcaagcttcagttaaatttgtatatataatctatcttacaagcaatgtcagtttgctgtctgcagGTATAGAGATTAATGATGAAGAGCTGGCAAGATTTGTTGAGCATGTGGATAAGGACAACAATGGGATTATTACTTTTGAAGAATGGAGAGATTTTCTTCT
upper sequence: GLYMA16G05100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G180971_T01 (Zea mays), 3'ss of exon 1
gactctaatttatttagtgtattattgttatgtgattttgatcttgtaatgtactttggtggttgtttcattcaata-agccaaactagtct--ctattgtagGAATTAAGATTGATGATGAAGAACTCGCCCGTTTTGTTGAGCGTGTTGATAAGGATAATAATGGTGTTATAACATTTGAAGAATGGAGGGATTTTCTGCT
||| || || | | || || | ||||| || || | | | | || |||| || || | | | ||| | ||| ||| || | |||||||||||||| || || | |||||||||| ||| |||||||| ||| ||||| |||| || ||||| || ||||| |||||||| |
gacactgat--aggaaacataa-atagctatgttccaaggagctggctgataaatctagtctttgtgatatgtcttacaagtatatcagtttaatgtttgcagGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGACAATGATGGTATTATTACTTTTGAGGAGTGGAGAGATTTTCTTTT
upper sequence: GLYMA16G05100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g00890.t01 (Vitis vinifera), 3'ss of exon 1
--gactctaatttatttagtgtattattgttatgtgattttgatcttgtaatgtactttggtggttgtttcattcaataagccaaactagtctctatt--gtagGAATTAAGATTGATGATGAAGAACTCGCCCGTTTTGTTGAGCGTGTTGATAAGGATAATAATGGTGTTATAACATTTGAAGAATGGAGGGATTTTCTGCT
| | || | || ||| || | || || || ||| | |||| | |||||| | ||||||| | ||||||| || ||||| ||||| ||||||||||| || || || || |||||||| ||||| || |||||||||||||| || |||||||||||||||||||| |||||||| |
ttgcttatatatacctttaaacggaattcttctcagagaatgg--ttccaattttagctggtcat--tttcatcctataagccgcagcagtctctcttttgtagGGATTAAAATTGATGATGAGGAGCTTGCTCGATTTGTTGAACGTGTGGACAAGGATAATAATGGGGTCATAACATTTGAAGAATGGAGAGATTTTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaatgtactttggtggttgtttcattcaataagccaaactagtctctattgtagGAATTAAGATTGATGATGAAGAACTCGCCCGTTTTGTTGAGCGTGTTGATAAGGATAATAATGGTGTTATAACATTTGAAGAATGGAGGGATTTTCTGCT
tctctatt CT-rich tract
attcaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gactctaatttatttagtgtattattgttatgtgattttgatcttgtaatgtactttggtggttgtttcattcaataagccaaactagtctctattgtagGAATTAAGATTGATGATGAAGAACTCGCCCGTTTTGTTGAGCGTGTTGATAAGGATAATAATGGTGTTATAACATTTGAAGAATGGAGGGATTTTCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - -aatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaact