Sequence
atgc intronic sequence ATGC exonic sequence...actgaattaataatatgcatttttgttaattttgatgagatcactgaatggctttgtgcttcattatcattttgaattgcaaaaatattgggcaataaagAAGCTACTACCGCTGCACGCATCACACGTGCAATGTGAAGAAACAAGTGCAAAGGCTATCCAAAGACACAAGCATTGTGGTGACGACTTACGAGGGAATT
Basic information
species | Glycine max |
transcript | GLYMA18G47350.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47350.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g53260.1 (Oryza sativa), 3'ss of exon 1
actgaattaataatatgcatttttgttaattttgatgagatcactgaatggctttgtgcttcattatcattttgaattgcaaaaa------tattg-ggca---ataaagAAGCTACTACCGCTGCACGCATCACACGTGCAATGTGAAGAAACAAGTGCAAAGGCTATCCAAAGACACAAGCATTGTGGTGACGACTTACGAGGGAATT
|||||| | | | | || || | | || | | | | || |||||| | ||| || |||| || || || ||||||||||| |||||||| ||||||||||| |||||||| |||||||| |||| |||| ||||| ||||| |||||||| || |||||||| |
---------gtaatatataagta-gatgtcttaagggataaaaatggacttttcctttatatatactcatttcctgtcgcataagtgcacgtattacaacatatatgcagGAGCTACTACCGGTGCACGCACCACACGTGCAACGTGAAGAAGCAAGTGCAGCGGCTCGCCAAGGACACGAGCATCGTGGTGACTACGTACGAGGGCGTG
upper sequence: GLYMA18G47350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G111354_T01 (Zea mays), 3'ss of exon 1
--------actgaattaataatatgcatttttgttaattttgatgagatcactgaatggctttgtgcttcattatcattttgaattgcaaaaatattgggcaataaagAAGCTACTACCGCTGCACGCATCACACGTGCAATGTGAAGAAACAAGTGCAAAGGCTATCCAAAGACACAAGCATTGTGGTGACGACTTACGAGGGAATT
| | | | | | | | | ||| | ||||| | | | | | || | | ||| || || || |||||||| || ||||| || |||||||||||||||||||| || ||||| |||| |||| || || ||||| ||||| || ||||||||||| |
ttgttcccgtgaactcactcgaacctagctacctctccgtccatgctaacactgtaaaacgtcgctgctgata--cgtgcgtgcgtgcgtgcatgc------atgcagGAGCTACTATCGGTGCACCCACCACACGTGCAATGTGAAGAAGCAGGTGCAGCGGCTGGCCAAGGATACGAGCATCGTGGTCACTACTTACGAGGGCGTC
upper sequence: GLYMA18G47350.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G015433_T01 (Zea mays), 3'ss of exon 1
actgaattaataatatgcatttttgttaattttgatgagatcactgaatggctttgtgcttcattatcattttgaattgcaaaaatattgggcaataaagAAGCTACTACCGCTGCACGCATCACACGTGCAATGTGAAGAAACAAGTGCAAAGGCTATCCAAAGACACAAGCATTGTGGTGACGACTTACGAGGGAATT
| || | | |||||| || | |||| ||| || | | |||||| | | | | ||| || | | | ||||| | || ||||||||||| |||||||| || |||||| | |||||||| || ||||| |||| |||| ||||| ||||| |||||||| || |||||||| |
--------gttgat-cgtctctttgttgatgctcatgaagtca-tgtcttatgcta-gcttcaatctgctgtggaaatgacgcactgt-gggca-tgcagGAGCTACTACCGGTGCACGCACCATACGTGCGACGTGAAGAAGCAGGTGCAGCGGCTGGCCAAGGACACGAGCATAGTGGTGACCACGTACGAGGGCGTG
upper sequence: GLYMA18G47350.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02150.t01 (Vitis vinifera), 3'ss of exon 1
ac-tgaattaataatatgcatttttgttaa----ttttgatgagatcactgaa----tggctttgtgcttcattatcattttgaattgcaaaaatattgggcaataaagAAGCTACTACCGCTGCACGCATCACACGTGCAATGTGAAGAAACAAGTGCAAAGGCTATCCAAAGACACAAGCATTGTGGTGACGACTTACGAGGGAATT
|| | | ||| || | | ||| || || |||| | | | || || || |||| || ||| | | | | || || |||||||| ||||| || |||||||| ||| ||||||||||||| || || ||||| || || || |||||| |||||||||| || || || || ||
acataatttaccaacacggattattattcgattcctttgttcgaaactctaaaatatcaactcaaaagttcacaattttttcttactttttatttttt---------agGAGCTACTATCGCTGTACACATCACACATGCGATGTGAAGAAACAGGTACAGAGGCTCTCAAAGGATACAAGCGTTGTGGTGACAACATATGAAGGCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatggctttgtgcttcattatcattttgaattgcaaaaatattgggcaataaagAAGCTACTACCGCTGCACGCATCACACGTGCAATGTGAAGAAACAAGTGCAAAGGCTATCCAAAGACACAAGCATTGTGGTGACGACTTACGAGGGAATT
attatcattttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgaattaataatatgcatttttgttaattttgatgagatcactgaatggctttgtgcttcattatcattttgaattgcaaaaatattgggcaataaagAAGCTACTACCGCTGCACGCATCACACGTGCAATGTGAAGAAACAAGTGCAAAGGCTATCCAAAGACACAAGCATTGTGGTGACGACTTACGAGGGAATT
- - - - - - - -tgcattt
- - - - - - - - - - - - - - - - tgatgag
- - - - - - - - - - - - - - - - - - - - -cactgaa
- - - - - - - - - - - - - - - - - - - - - - - - -ggctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata