Sequence
atgc intronic sequence ATGC exonic sequence...ggcttatattttataattgtaacgtaaggattacctgtggtttctttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
Basic information
species | Glycine max |
transcript | GLYMA01G39950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 4
--ggcttatattttata-attgtaacgtaaggattacctgtggtttctttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
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cagtgttatagcaaatttattggttttagaagactatata-agttttcttatatttgaaaatg--tggatagttttatctgcaaacttattttctttatccagATACTTCAAAGGGCCTGAATTGCTGGTTGACTTCCAAAGTTATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATG
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 4
--ggcttatattttataattgtaacgta-aggattacctgtggtttctttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
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tgtggttttctttgatttctgaaatttttatagtaagatgggagatcctaagaattcagattttttcgtaaggtttgaagt---tcctttccttgttactcagATACTTTAAGGGGCCAGAACTTCTTGTTGATTTGCAAGATTATGATTATTCTTTGGATATGTGGAGCCTTGGTTGCATGTTTGCGGGAATG
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 4
ggcttatattttataattgtaacgtaaggat-tacctgtggtttctttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
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attttctatagcatagacttgatttgtttgtataaatatcttgcttgctgtataggcaattttctaggatg-ttaatatttgcatgttccctgtaatccagATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATG
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 5
ggcttatattttataattgtaacgtaaggattacctgtg-gtttctttttaaatgtcactgacccaacacaatt-gtcatgtgtcctgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
||||| || | | || | ||| | | | || ||| | ||| | | ||| | ||| || ||||| |||||||| ||||| ||||| | || || ||| | ||||| ||||||||||| | |||||||||||| | || |||||||||||||| |||
-acttat-ttctttcatgctccagtaggtactctgaatgcgttgtcaacttcatgctgtttttttcttgccatttaaaacttgttttggttttgggaaatagATACTTCAAGGGCCCTGAGTTGCTGGTGGATCTCCAAGATTATGACTACTCCCTTGATATGTGGAGCTTGGGATGCATGTTTGCTGGCATG
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 4
ggcttatattttataattgtaacgtaaggattacctgtggtttctttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttc--tcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
|| ||| | || | || ||||| | | ||| | | | ||||| ||| | | |||||||||| || || || || || || || || |||| ||||| || ||||| | || ||||||||||| ||||||||||| |||||||||
-----------------------gtgtggaaaaggcgttgc------ttgaatgtgat---ctcaattccaataatttgtgtgctgtcgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 4
ggcttatattttataattgtaacgtaaggattacctgtggtttctttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttc--tcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
|| ||| | || | || ||||| | | ||| | | | ||||| ||| | | | |||||||||| || || || || || || || || |||| ||||| || ||||| | || ||||||||||| ||||||||||| |||||||||
-----------------------gtgtggaaaaggcgttgc------ttgaatgtgat---ctcaattccaatcatttgtgtgctgttgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
cactgac putative branch site (score: 2)
tcctgcttttgtttct putative PPT
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcttatattttataattgtaacgtaaggattacctgtggtttctttttaaatgtcactgacccaacacaattgtcatgtgtcctgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - acctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgct