Sequence
atgc intronic sequence ATGC exonic sequence...tgcaagtattttttatgtgcattttctgttgcatgtatttacctcgtatagtggaaggtaaaaggggaagaatttttaatgaatattcattttactcaagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT
Basic information
species | Glycine max |
transcript | GLYMA08G26860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G26860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g00420.t01 (Vitis vinifera), 3'ss of exon 4
--tgcaagtattttttatgtgcattttctgttgcatgtatttacct-cgtatagtggaaggtaaaaggggaag--aatttttaatgaatattcattttactcaagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT
| | | | | | || || | || |||| | |||| | | || | |||| ||| || ||| |||||||||||||| || ||||| |||||||| |||| ||||| ||||| ||||| ||||| | ||||||||||| | |||||| | |||||||||||||
aatatttgctctaaggaaacaaaatatccattatgaacagatattaatgtattgctgaagattttacatcaatttagttttaaatctatggctcttt-----aagTTTCAAGGTTTCAATTGGGAAAGCTGGAGGAGGCAGTGGTACCTGGAGTTAGCGCCTAAAGCTGCTGACTTATCCCAATGTGGGATAACAGCAGTGTGGT
upper sequence: GLYMA08G26860.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S100_191V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------tgcaagtattttttatgtgcattttctgttgcatgtatttacctcgtatagtggaaggtaaaaggggaagaatttttaa--tgaatattcattttact-caagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT
| | | | | | || | | | ||| |||| | | || | | | | || | || || |||| ||| ||||| | | ||||||||||||| |||||||||||||||||| ||| |||| ||||| | |||| ||| | | || | || || || || | ||| | | |||
gtacgtactcaccgtatccgattcctgcgaacttgaactatatgt-gcatagacctgacttctcttttatatcttatgtacatctgtgttaacaacgtgaacattgattttgatgccagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAGTGGTGGCTGGAGATGTCAGCGAAAGCCTCAGATCTTTCCAAATGCGGAATCACAACTATCTGGC
upper sequence: GLYMA08G26860.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S342_20V6.1 (Physcomitrella patens), 3'ss of exon 7
-tgcaagtattttt-tatgtgcattttctgttgcatgtatttacctcgtatagtggaaggtaaaaggggaagaatttttaatgaatattcattttactcaagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT
| | || || || || ||| || || | || |||| | | | | | | | ||||| | | | || ||||||||||||| |||||||||||||||||| ||| |||| |||| | ||||||| | | || | | || ||||| | || || | |||
ctatatgtgttgttatactaacatctt-tgcgatcgtttcgcctcttgtatgctctactcttgacatctgtgttgatatcgtgaat-tgcttcttgtgtcagTTTCAAGGTTTCAACTGGGAGAGCTGGAGACGGCAATGGTGGTTGGAGATGTCAGCTAAGGCCTCGGATCTTGCAAAATGTGGAATAACCACAATCTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatagtggaaggtaaaaggggaagaatttttaatgaatattcattttactcaagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT
ttttaat putative branch site (score: 3)
ttcatttt putative PPT
aagaatttttaatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcaagtattttttatgtgcattttctgttgcatgtatttacctcgtatagtggaaggtaaaaggggaagaatttttaatgaatattcattttactcaagTTTCAAGGTTTTAACTGGGAGAGCTGGAGAAGGCGCTGGTATCTGGAATTAGCAGCTAAAACAGCTGACTTATCTAATTGTGGGGTGACAGCAGTGTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
tgcaagt
- - - - - - - - -tgcattt
- - - - - - - - - - - - - - - gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - -tggaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggaag