Sequence
atgc intronic sequence ATGC exonic sequence...ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
Basic information
species | Glycine max |
transcript | GLYMA13G03280.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 4
ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
||| || | || || | ||| ||| || ||| | || || || || |||||| |||||||||||| ||| ||||||| || ||||||||||||| | | ||||||||||| ||||||||||| ||||| ||||| |||||||| || |
------------------gtatgttacgataatatgccaaagcaatctgtgctgtgaagcc-catgataacttttctttaacaacaccaatttattgaagGATGATGAAAGAGGCATGCGGTGGTTCTATTCTGGTGACATTGGACGTTTGCATCCAGATGGTTGCCTTGAAATTATTGACCGTAAGAAGGACATAGTCA
upper sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 9
-------------ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
|| || | | | | | || | | | | | | | || | | || || ||| ||| | | || | |||||||| ||| |||| ||| ||| | ||||| || |||||||||| ||| | | || |||||||| ||||||||||||||||| ||||||||||| ||||| |
gtatgttgtcttgttaccaatatgttcgatgactacttcacggctcatagtaataaccttctatccacaataatttacat--aacctttgtacctcat--ttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
upper sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 7
ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
| | ||| | || | | || ||| | || | | | | ||| || | |||| |||||||||||||||||| ||| | ||||| ||| |||| ||||||||| | | || ||||||||||| |||||||| || || || || ||||| || || |
----------------gtgtgtttgcaacaaatacccagtgcccaggaaagtgtttattgtggctactttacctgaacactatgcatatttt----gaagGTTGATGAAAGAGGCATGCGATGGTTCTACTCTGGCGACATTGGGCGCTTGCACCCAGATGGATGTCTTGAAATTATCGACCGCAAGAAGGATATAGTCA
upper sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 9
---ttgtcagtttttgtgtttttatttttattttatgtggggggaggag----agaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
| || | | | |||| || || | | || || | || | | | | ||| || | | || |||||||| |||||| | ||| ||| | ||||| || |||| ||||| || | | ||||||||||| ||||||||||||||||| ||||| || || || || |
gtatggtgttctcctaccaatatattcatagattgtttcaggcattgaactttaacttcttcacactttctgtaacaataaccacacaccacatatattatgtgaagGATGATGAGAAAGGTATGCGATGGTTCTATTCTGGAGACATCGGACGGTTCCATCCAGATGGCTGCCTTGAAATCATTGACCGTAAGAAAGATATCGTGA
upper sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaa-gctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
|| | | || | | | | || | | |||| | || | |||| | || | | || ||| || || | ||| | ||||||||||||| ||||||||||||||||||||||| || ||||| ||| ||||| | ||||| ||||||||||| ||||| |||| ||||||||| ||||
gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgaccaaagaataattgtaaactggacatgtaataaactttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA
upper sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ26722 (Selaginella moellendorffii), 3'ss of exon 8
ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtac-tttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
| | || || | | | || ||| | || | | ||||| |||||||||||| || || || ||||| ||||| ||||||||||||||||| | | ||||| ||||| ||| | ||||| | || || || |||||||||||||
---------------------------------------------gtacaacttttcagtttcct-tgaagcgttcatgtttaattcgtttttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTA
upper sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 8
ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgt--actttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
| | || || | | | || ||| | ||| | ||||| |||||||||||| || || || ||||| ||||| ||||||||||||||||| | ||||| ||||| ||||| ||||| | || || || |||||||||||||
---------------------------------------------gtacaacttttcagtttcct-tgaagcgttcatgcttaattgggtttttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
agctaaa putative branch site (score: 3)
tttttactttgtactt putative PPT
aaattaaatgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA