Sequence
atgc intronic sequence ATGC exonic sequence...gctcccccacacaccgtatacctagtcatcatgttgttcttcataagtatttggaatccttttctttattttactaattcaccgccacggtctctttcagCAATATGTTAAAGGTATATCAACAACTGGGATGCAATCTAACTATGGTTTCGATGGTCAACTCAATGCATGTTGGACACATAAAATGACTGAAACAGAGA
Basic information
species | Glycine max |
transcript | GLYMA19G16680.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G16680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G079938_T04 (Zea mays), 3'ss of exon 6
gctcccccacacaccgtatacctagtcatcatgttgttcttcataagtatttg-gaatccttttctttattttac-taattcaccgccacggtctctttcagCAATATGTTAAAGGTATATCAACAACTGGGATGCAATCTAACTATGGTTTCGATGGTCAACTCAATGCATGTTGGACACATAAAATGACTGAAACAGAGA
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-aatataaacatatta-gtaggtagacaccagaatgaagacaacatacatacatgcatcaacctattcatggaaggtttatctgtaccgtgtcttctttcagGAATATGTGAAGGGCATATCGTCGACAGGGATGCAATCTAATTGTGGTTTTGAAGGGCAAATCAATGCATGTTGGACTCACAACATGACTACTAAGGAGC
upper sequence: GLYMA19G16680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G093441_T02 (Zea mays), 3'ss of exon 5
-gctcccccacacac-cgtatacctagtcatcatgttgttcttcataagtatttggaatccttttctttattttactaattcaccgccacggtctctttcagCAATATGTTAAAGGTATATCAACAACTGGGATGCAATCTAACTATGGTTTCGATGGTCAACTCAATGCATGTTGGACACATAAAATGACTGAAACAGAGA
||| | | || || || | || | | | || | | ||| ||| | | | || | | ||||||| ||||||| || || ||||| |||| ||||||||||| || | |||||| || || ||| | |||||||| ||||| || ||||||||| | ||
caactataaacatatatgagtaggtacacactaaaatgaagacaacatgcatgcagcaacctattcactgaagtttca--tctgtactgtatttgctttcagGAATATGTGAAGGGCATATCGTCAACAGGGATGCAATCCAATTGTGGTTTTGAAGGGCAAGTTAATGCATGCTGGACTCACAAAATGACTACTAAGGAAC
upper sequence: GLYMA19G16680.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0098g01700.t01 (Vitis vinifera), 3'ss of exon 6
-----gctcccccacacaccgtatacctagtcatcatgttgttcttcataagtat-ttggaatccttttctttattttactaattcaccgccacggtctctttcagCAATATGTTAAAGGTATATCAACAACTGGGATGCAATCTAACTATGGTTTCGATGGTCAACTCAATGCATGTTGGACACATAAAATGACTGAAACAGAGA
||| | | || ||| ||| ||||| | | || ||| | | | | | | || ||| ||||| | | ||| ||||||| |||||||||||| | |||||||||||||| || ||||||| || |||||| | |||||||| ||||||||||||||||| || ||||
aaaccgctgtcttattgacatcataatagctcaattaattgttggcagtgaccatgttgcattgcggattctaaattcacttgaaacccgcc------ttatgcagGAATATGTGAAAGGTATATCATCGACTGGGATGCAATCCAATCATGGTTTTGAAGGTCAAATTAATGCATGCTGGACACATAAAATGACAAAAGCAGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatttggaatccttttctttattttactaattcaccgccacggtctctttcagCAATATGTTAAAGGTATATCAACAACTGGGATGCAATCTAACTATGGTTTCGATGGTCAACTCAATGCATGTTGGACACATAAAATGACTGAAACAGAGA
tactaat putative branch site (score: 1)
tctctttc putative PPT
ttttctttattttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctcccccacacaccgtatacctagtcatcatgttgttcttcataagtatttggaatccttttctttattttactaattcaccgccacggtctctttcagCAATATGTTAAAGGTATATCAACAACTGGGATGCAATCTAACTATGGTTTCGATGGTCAACTCAATGCATGTTGGACACATAAAATGACTGAAACAGAGA
-ctccccc
- - - - acacacc
- - - - - - - - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgccac