Sequence
atgc intronic sequence ATGC exonic sequence...gaagttagatactttgattttgggtatgggatttcaccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttatttctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
Basic information
species | Glycine max |
transcript | GLYMA17G00480.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g13820.2 (Oryza sativa), 3'ss of exon 8
-gaagttagatactttgattttgggtatgggatttcaccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttatttctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
||| | ||| | | || ||||| | | ||| | | ||| | | | || | | | | | | | | | |||| |||||||||||||||||| |||||||||||||| || || | ||||| || || || || | ||||| ||||||||| | | |||||| || |
gttagtaaagagcttcaaacctactta---gatttta--atcataccttcctaaactgcacaagcaattacaataacaatatactgtct-tgtataaatagGGGTCTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGGAAATTCCCAGAGAGAATTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAA
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
gaagttagatactttgattttgggtatgggatttcaccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttatttc--tttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
||||| | | | | |||||| ||| | || | | | || | | || | | | || | ||| | |||| |||||||||| ||||||| || ||||| ||||| ||||| | || ||||| || |||||| | ||||| || ||||| || ||||||||||| |
---gttagtga---taagctcaagtatggtcttt-atatatacctta-attagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 8
gaagttagatactttgattttgggtatggg-atttca----ccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttatttctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
| |||| |||| ||| | || | || | | | || | | | | | | | || ||| | ||| ||| | | ||||| | |||||||||||||||||| ||||||||||| ||||| || ||| | |||||||| ||||| | || ||||| |||||| | |||||||| || |
-gatatagagtttttgtacttgtctgtgttcagtttatgggctgaagtcccttttggagcttggcaaatgtttttctcaaaacttttt----gattcttgttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAA
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
gaagttagatactttgattttgggtatgg-gatttcaccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttat-----ttctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
|| | || ||| || ||| |||| || | | ||| | || ||||||| | | || | |||| | || || | ||||| | |||||||||||||||||| ||||||||||| ||||| || || | ||||| | ||||| | || ||||| |||||| | ||||||||||| |
-----aaggtttttgaattgcatgtctggtgattgtgcccgttca-tgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 8
gaagttagatactttgattttgggtatgggatttcaccaatgtactgtacaa--aaatccttttttttctgcatc--taaattctttcctttattt-ctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
|| | | |||| | | | ||||| | || ||||| |||| || | | ||| || | || || | |||| |||||||||||| ||||||||||||||||| ||||||||||| ||||| || ||||| |||||||| || ||| | || | ||| ||||| |||||||||||||| |
----ttcta-gcattgactgctatcaaccttgtgcaccattagacattacaacagaatctgttctactgcccattattagctgctgtcataaattttctttgcagGGTAGCGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAACAGGATCAAGCAGCTACCTTTAGATAAACATTTTGATATAAACAATGTCAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacaaaaatccttttttttctgcatctaaattctttcctttatttctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
atctaaa putative branch site (score: 3)
ttctttcctttatttc CT-rich tract
aaaaatcctttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagttagatactttgattttgggtatgggatttcaccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttatttctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - -gggtatg
- - - - - - - - - - - - - - - - -tcaccaa
- - - - - - - - - - - - - - - - - - - - - - - - acaaaaa