Sequence
atgc intronic sequence ATGC exonic sequence...tcttttcaagaccatgtttgacagtgttagttgtttggtgcattctgattatttaaattcactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
Basic information
species | Glycine max |
transcript | GLYMA02G00550.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 4
-----tcttttcaagaccatgtttgac--agtgttagttgtttggtgcattctgattatttaaattcactttcatctcatagacc-tcacagtgagtt-----------tgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
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gtaagtttgttctttagaatctttcaccaataatttcttatcacaaacatgatacatatttaaatgttgggctttttcaaacttcattattgtgattcatcttttctactatctggcagATGCTAAAGTTCAAAGATAACAATATTAACAATGAGGGAATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 4
tcttttcaagaccatgtttgacagtgttagttgtttggtgcattctgattatttaaattcactttcatctcatagacctca--cagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
|| || |||| | || | ||| || | | | || | | || | || ||| | ||||||||| ||||| | | ||| | || ||||| || | || || || |||||||||||||| || || ||||| |||||||||| ||||||||||
-------------------------gtaagccttttgtcttgattc--ttttgtaagttgccctgaaattctttaatctaacccatctctactgtttggcagATGCTAAATTTCAAGGATAACAATATAAACAATGATGGGATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
tcttttcaagaccatgtttgacagt-gttagttgtttggtgcattctgattatttaaattcactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
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---------------gtaaggcagttactagatcttatgtggaatagaggtgtgt--gtccatcttcatttactgatactattcatggaa----attgcagATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 4
tcttttcaagaccatgtttgacagtgttagttgtttggtgcattctgattatttaaattcactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
|| ||| |||| | || | ||| | | |||| ||| || | || ||||||||||| || ||||| || || | ||| | ||||| ||| | | |||||||||||||| || ||||| |||||||||||||||||||| |||||
-----------------------gtaagagtcttttgctcactttttatttctagtgataacttgtctctaatgatttt---------ttgactttgcagATGCTTAACTTTTCGAACGATGTATTGAATGACGAAGGGAGATTAAGAACGGTTCTTGATGTCGGATGCGGAGTTGCGAGTTTTGGAGCTTACCTTCTCG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
tcttttcaagaccatgtttgacagtgttagttgtttggtgcattctgattatttaaatt-cactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
|| | ||| | ||| | || | || | || ||| ||||||| | || | || | || |||||||| || | | | || | || || || | ||||| || |||||||| | |||||||| || ||||||||||||||||||| ||||||| | |
---------------gtaaggaagttacacttggtgtttgtacaa-gagaacgtatattattctttcatttgctaattgtattcttgga--aatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 4
tcttttcaagaccatgtttgacagtgttagttgtttggtgcatt--ctgattatttaaattcact------ttcatctcatagacctcacagtgagtttgtattg-cagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
| ||| || | | | | ||| |||||| ||| | | ||||| | ||| || | ||| || ||| | ||||| || ||||||||||| |||||| || ||||||| || || | ||||| | || || ||| ||||||||||||| |||||||| ||||||||||| ||||||||||
--------atttcattttagggatttctggttctttggtaaattattttagtattttcttctactgcatggttgaagcaataattctatttgtg-gcttgtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACTGTTTTTGATGTTGGCTGTGGTGTTGCAAGTTTTGGAGCCTATCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattatttaaattcactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
acctcac putative branch site (score: 3)
atttaaattcacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttttcaagaccatgtttgacagtgttagttgtttggtgcattctgattatttaaattcactttcatctcatagacctcacagtgagtttgtattgcagATGCTCAATTTTTCACACCATAATCTCAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGCGGTGTTGCGAGTTTTGGAGCTTATCTTCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - -ccatgtt
- - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcaca