Sequence
atgc intronic sequence ATGC exonic sequence...gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgcatagtagctaactcattttttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
Basic information
species | Glycine max |
transcript | GLYMA13G01170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g14770.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------------gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagttt------gaagttctttgcatagtagctaactcattttttgtgc-agGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
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gtatgtgctgtaacttcactatgattttgcataattattatcactgacaaattctaagtacagctgttgtttaatgt-tacttttatgttactatacaagtcacgttgttgagaaacacttcattcattagacaccttctcttgtatgttagATTGGGCTTCTCGAGTTTATTTTTCAGACAATGGATCTACTGCAATTGAAATTGCTTTGAAGATGGCATTTCGTAAATATGCATGTGACCATGGGATTAT
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G102156_T01 (Zea mays), 3'ss of exon 5
gatgtttgccaatgctcattgtta-tctattgaa--tgatgata-cattattt-tatgagcagtttgaagttctttgcatagtagctaactcattttttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
| | | | | | ||| | ||||| | | ||||| ||| || | | || | | |||| | | || | | |||| | |||| ||||||||||| |||| ||| ||||||||||| || ||||||||||||||||| |||||||| ||||||||||||||| ||||||||||| ||||
--tttatttctttatttcttgcaactctatccacatcgctgatagcatcgttcctttttgcgtgcctatcatatttgtgtcacaacttcccctttttct---cagGATGGGCTTCTCGAGTCTATTATTCAGACAATGGATCCACTGCAATTGAAATTGCTCTGAAGATGGCATTTCGTAAATTTTCTCTTGATCATGGAATTAT
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 5
gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgcatagtagctaactcattttt-tgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
||| | || ||||| ||| || ||| || | ||| | | ||| | ||| | |||||||||||||||||| ||| || ||||| |||||||| |||||||| |||||||| | |||||||| |||||||| |||| ||| |||||| ||
--------------------gtttctaaacttgctctgtcacattgtttaat------tttcaaa--cattgggggatggttaattattttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 5
gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgc-atagtagctaactcatttt----ttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
| || | | ||| | | || | | || | | | | ||| ||| | | || | || | ||| |||| || || |||||| ||||||||||| || | |||||||| ||||||||||||||||||||| ||||||| |||||||| ||||| ||||| ||| |||||||||| | ||
---gattttctggatttgttg--aagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ25518 (Selaginella moellendorffii), 3'ss of exon 5
gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgcatagtagctaactcattttttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
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------------------------------------------------gtaaacactgctctggcttaattatatcttacgaaacttttattttttcaagGCTGGGCACATAGAGTTTATATTTCTGACAATGGATCGACCGCTACTGAAATTGCTCTCAAAATGGCTTTGAGAAAATATGCTGTTGATCATGGCTTTCT
upper sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ22227 (Selaginella moellendorffii), 3'ss of exon 5
gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgcatagtagctaactcattttttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
|| | | | | || || || |||| |||||| | ||||||||| | ||| |||| ||||||||||| || || | ||||||||||||||| ||||| || | |||| | ||||||||||||| || |
------------------------------------------------gtaaacactgctcttgcctaattatatcttacgaaactt-ttttttttcaagGCTGGGCACACAGAGTTTATATTTCTGACAATGGATCGACCGCTACTGAAATTGCTCTCAAAATGGCTTTGAGAAAATATGCTGTTGATCATGGCTTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttatgagcagtttgaagttctttgcatagtagctaactcattttttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
agctaac putative branch site (score: 2)
ctcatttttt CT-rich tract
tcatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgcatagtagctaactcattttttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- tgtttgc
- - - - - aatgctc
- - - - - - - - - - - - - - -tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaact