Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttgatatctacttcttgtgaatgaatgattatgaacttttcaatcattaacatgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
Basic information
species | Glycine max |
transcript | GLYMA19G42790.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagcttgatatctacttcttgtgaatgaatgatt--atgaacttttcaatcattaacatgtgaagcgcaatagatccattgttttgcc-taaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
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----------------ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
upper sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00570.t01 (Vitis vinifera), 3'ss of exon 12
---gtaagcttgatatctacttcttgtgaatgaatgattatgaacttt-tcaatcattaacatgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
||| | || | || ||| ||||| | | | || | |||||| | ||||| | | |||| | | | ||| || | ||| | | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| |||| || | || |||||||||||| |
acactaaattccatgtttatagctt--gaatgttagctcacaaaataaatcaatcttattcatgtagtgggtaata----taatttcttgactga----------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC
upper sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0121g00080.t01 (Vitis vinifera), 3'ss of exon 11
--gtaagcttgatatctacttcttgtgaatgaatgattatgaacttt-tcaatcattaac-atgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
||| | || | || ||| ||||| | | | || | |||||| ||| |||| | | |||| | | | ||| | | ||| | | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| |||| || | || |||||||||||| |
cactaaattccatgtttatagctt--gaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaata----taatttcttgattga----------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC
upper sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00550.t01 (Vitis vinifera), 3'ss of exon 8
--gtaagcttgatatctacttcttgtgaatgaatgattatgaacttt-tcaatcattaac-atgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
| || | || | ||| ||||| | | | || | |||||| ||| |||| | | |||| | | | ||| || | ||| | | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| |||| || | || |||||||||||| |
gtgagaggcttatgctaatagctt--gaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaata----taatttcttgactga----------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAAATGATGGTACCGTATCAC
upper sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00500.t01 (Vitis vinifera), 3'ss of exon 11
--gtaagcttgatatctacttcttgtgaatgaatgattatgaacttttcaatcattaac-atgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
||| | || | ||| |||| | | | | || |||||| ||| |||| | | |||| | | | ||| || | ||| | | |||||||||||||||| ||||| || || || ||||||||| ||||||||| |||||||| ||||| ||||| |||| || | || ||||||| |||| |
cactaaattccatgtttacagcttgaaagttagctcaca-aaataaatcaatctttattgatgtagtgggtaata----taatttcttgactga----------attccttt-cagGCTATAATGGAGGTCGGAGAGGTAATACAATTTTATGATACTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCATATCAC
upper sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00540.t01 (Vitis vinifera), 3'ss of exon 9
--gtaagcttgatatctacttcttgtgaatgaatgattatgaacttt-tcaatcattaac-atgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
||| | || | || ||| ||||| | | | || | |||||| ||| |||| | | |||| | | | ||| || | ||| | | |||||||||||||||||||||| || || || |||||||||||||||| || |||||||| ||||| ||||| |||| || | || ||||||| |||| |
cactaaattccatgtttatagctt--gaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaata----taatttcttgactga----------attccttt-cagGCTATAATGGAGGTTGGAGAGGTAATACAATTTTATGATTCTGATAAGCGCTTTCCTGCATGGGGATTTGGGGGAAGGACAATTGATGGTACCATATCAC
upper sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0030g00600.t01 (Vitis vinifera), 3'ss of exon 9
--gtaagcttgatatctacttcttgtgaatgaatgattatgaacttt-tcaatcattaac-atgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
||| | || | || ||| ||||| | | | || | ||| || ||| |||| | | |||| | | | ||| | | ||| | | |||||||||||||||| ||||| || || || ||||||||||||||||||| |||||||| ||||| ||||| |||| || | || |||||||||||| |
cactaaattccatgtttatagctt--gaatgttagctcacaaaataaatcagtctttattgatgtagtgggtaata----taatttcttgattga----------attccttt-cagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
gcctaac putative branch site (score: 2)
tttatct putative PPT
agtatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttgatatctacttcttgtgaatgaatgattatgaacttttcaatcattaacatgtgaagcgcaatagatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG