Sequence
atgc intronic sequence ATGC exonic sequence...ctatcatgcacaacccagtgataagctagtatttagatttgatatgccaagtgcaaaaatgatattatttaattttaaatataaaattgtggttttatagGTGATCGCAAGGACCAGAAAATTCTTGAAAGTCTTAGAGCTGAAAGGAAGGCAAAAATTGATGAGCTCAAAGAGAAGACAAATTATTACATTACTCAACA
Basic information
species | Glycine max |
transcript | GLYMA17G29620.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g41990.1 (Oryza sativa), 3'ss of exon 2
ctatcatgcacaacccagtgataagctagtattta-gatttgatatgccaagtgca-aaaatgatattatttaattttaaatataaaattgtggt--tttatagGTGATCGCAAGGACCAGAAAATTCTTGAAAGTCTTAGAGCTGAAAGGAAGGCAAAAATTGATGAGCTCAAAGAGAAGACAAATTATTACATTACTCAACA
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-agatatttactatt---ttatatgtcaatttacatgatatagcatttaatctgtatgatgtgttagtatactctattcacttcctatttgtatctgttcacagTTGAGCGGAAAGACCAGAAGACACTTGAAAAGCTGAGAGCTGAGAGGAAGGCCAAGATTGATGAGCTAAAAGAGAGAACTAATTATTACCTCACCCAACA
upper sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0215g00090.t01 (Vitis vinifera), 3'ss of exon 3
-ctatcatg-cacaacccagtgataagctagtatttagatttgatatgccaagtgcaaaaatgatattatttaattttaaatataaaattgtggttttatagGTGATCGCAAGGACCAGAAAATTCTTGAAAGTCTTAGAGCTGAAAGGAAGGCAAAAATTGATGAGCTCAAAGAGAAGACAAATTATTACATTACTCAACA
| | || | ||| | | || | |||| ||||| | | | || | | | | | |||| ||| | | || || ||||||||| |||||||||||||||| ||| ||||| ||| | ||||||||| | ||||| ||||||||||| || || ||||||||||| || |||||||||||
agtttgatatctcaaactttcaagaatttggtatact-atttg-tgttctggtcaaaattagtacagcaatgaattctaatgtaatgaacatgattgtatagGTGACCGCAAGGACCAGAAAACTCTGGAAAGGCTTCGGGCTGAAAGGCAAGCAAAGATTGATGAGCTTAAGGAAAAGACAAATTACTATATTACTCAACA
upper sequence: GLYMA17G29620.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0033g01150.t01 (Vitis vinifera), 3'ss of exon 4
ctatcatgcacaacccagtgataagctagtatttagatttgatatgccaagtgcaaaaatgatat-tatttaattttaaatataaaattgtggttttatagGTGATCGCAAGGACCAGAAAATTCTTGAAAGTCTTAGAGCTGAAAGGAAGGCAAAAATTGATGAGCTCAAAGAGAAGACAAATTATTACATTACTCAACA
| | | | | | | | | | || | ||| | || | || | | | | | |||| | || || || |||||| |||| ||| ||||||| ||| || | ||| |||| ||||| |||||||||||||| |||||||||| |||||||||||| | || |||||
ttttagagtttgatatgtcaaactgttgacaatctactatg-tgtgctctggtcatatttggcgtatcatggaactgaaattttttcacatgattgtacagGTGACCGCAGGGATCAGAAAACTCTAGAGCGCCTTCGAGCCGAAAGACGAGCAAAAATTGATGAACTCAAAGAGAGGACAAATTATTATACCACACAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccaagtgcaaaaatgatattatttaattttaaatataaaattgtggttttatagGTGATCGCAAGGACCAGAAAATTCTTGAAAGTCTTAGAGCTGAAAGGAAGGCAAAAATTGATGAGCTCAAAGAGAAGACAAATTATTACATTACTCAACA
atttaat putative branch site (score: 4)
atattatttaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatcatgcacaacccagtgataagctagtatttagatttgatatgccaagtgcaaaaatgatattatttaattttaaatataaaattgtggttttatagGTGATCGCAAGGACCAGAAAATTCTTGAAAGTCTTAGAGCTGAAAGGAAGGCAAAAATTGATGAGCTCAAAGAGAAGACAAATTATTACATTACTCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - catgcac
- - - - - - - - - - - - - - - - - - - - - tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - -agtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatataa