Sequence
atgc intronic sequence ATGC exonic sequencegtacgttttattgttgtattttcaattaggatgaatgcaatctctcaatgtcatgatatactcacttttatgacttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
Basic information
species | Glycine max |
transcript | GLYMA16G15820.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 14
gtacgttttattgttgtattttcaattaggatgaatgcaatctctcaatgt-catgatatactcacttttatgacttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
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gtaagag--attgctgcattttgttgaaggccttttgctttgttacggtgaatgtttttgtcctactacaaatacgaattcacattttctctt-cagCGTGTCGAAGTGGAGCGCACATTGACTGATTCACAGCGTGATGAATTTGAGGACATGCTACGTGCATTGACATTGGAGAGAAGTCAGATAAAGGAGGCTA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 13
------------------------gtacgttttattgttgtattttcaattaggatgaatgcaatctctcaatgtcatgatatactcacttttatgacttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
| | || |||||||| | | || | ||| ||| || ||| | | || | || ||| | | | ||||| || || || | ||| ||||||| ||||| | |||||||||||||| |||||||| ||||| ||||||||||||||||| |||||||| || |
gtaaataactgttagacgtactcagagcattaaattgttgtttcattgttt--gttgatgtcaaataaataa----atggtgttct-gttacaatactaaatttctgatccgtccttcagCGTGTTGAAGTGGAGCGTACATTGACTGACTCACAGCGTGATGAATTTGAGGACATGCTGCGAGCTTTGACATTAGAGAGGAGCCAAATAAAAGACGCCA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 12
gta--cgttttattgttgtattttcaattaggatgaatgcaatctctcaatgtcatgatatactcacttt-tatg------acttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
||| | | || | || || |||| | | | | | | | | || || | || || || || ||| || ||||| | || ||| || || ||||| ||| | ||||||||||| || ||||| ||| |||||||| | || ||||| ||||| ||||||||||| ||||
gtaatcttcttgcactcttacttctaatttatttatttctttttcttttgttagctaagttgttcttttggtgtgcgggatacctgacactgttaaatcttacagCGTGCGGAAGTTGAGAGGACTCTGACCGATCCTCAGAGGGATGAGTTCGAGGACATGTTGCGTGCTCTTACTTTAGAAAGGAGTCAGATAAAAGAAGCTA
upper sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 12
---------------------------------------------------------------------gtacgttttattgttgtattttcaattaggatgaatgcaa-tctctcaatgtcatgatatactcacttttatga---------cttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
| || ||| || || | | | || || || || ||||||| | | | | | |||||||| ||| ||| || | | ||||| || |||| ||| | ||| |||||||| |||||||||||||||||||||||||| |||||||||| |||||||| ||||| |||||||| || ||||
gtacatataaatacatacatatatgcatacatacatacatacgtgtatatatatatatatatatatattccaatttctatggtggtcctgtta--taccctgtttggaaatctctcatttagagaacttgtcaaattttatgattaaacccccttttttctgttaacttgcacagCGTGTGGAGCTGGAACGGACATTGACTGATCCACAGAGGGATGAATTTGAGGATATGTTGCGTGCTTTGACATTAGAAAGGAGTCAGATAAAGGAAGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctcaatgtcatgatatactcacttttatgacttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
ttttgattgaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttttattgttgtattttcaattaggatgaatgcaatctctcaatgtcatgatatactcacttttatgacttgttttgattgaatattgcagCGAGTAGAGCCTGAAAGAACACTGACTGATGCACAGAGGGATGAATTTGAGGATATGCTGCGTGCTTTAACATTAGAGAGGAGCCAGATAAAAGAGGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG