Sequence
atgc intronic sequence ATGC exonic sequence...atttattattgttgctgctaattattataattattaatttattaattacttataagtgtttctgctgactagtgacatttgaaattcataaattttgcagATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
Basic information
species | Glycine max |
transcript | GLYMA20G16860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 2
----atttattattgttgctgctaattattataattattaatttattaattacttataagtgtttctgctgactagtgacatttgaaattcataaattttgcagATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
| | | || | | | ||| || || | || |||| ||| || |||| | ||| | ||| || | ||||| |||||||| || || ||| |||| |||| |||||| ||| ||||||| || |||||||| | ||| ||||| || || ||||| |||||||||||||||
gataaagtgtaatcagttttatttgaaattccaacactt--ctaatgaattttttaattgtttttcagatgatt--tgatgaatggtttatctaaatgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S53_93V6.1 (Physcomitrella patens), 3'ss of exon 2
atttattattgttgctgctaattattataat-tattaatttattaattacttataagtgtttctgctgactagtgacatttgaaattcataaattttgcagATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
|| | ||| | | | || | || | |||| | |||| | | ||| | | ||| | | | || | | | | ||||| || | | || ||||||| ||||| ||| ||||||||||| ||||||||||||| || || || |||||||| || || ||||| ||
tttcacgattatgtaatcatgtagtttttatgtgttaaagaaataatcaaaagacgggatttgtaat-acttgcaattcgttaagtaccatgtctctccagATATTGCGGCAATTAAAGCATGAGAATATCATTGAAATGCTTGATGCCTTTGAAAGCCCCCAGGAGTTCTGTGTTGTGACTGAGTTTGCTCAG
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ37043 (Selaginella moellendorffii), 3'ss of exon 2
atttattattgttgctgctaattattataattattaatttattaattacttataagtgtttctgctgactagtgacatttgaaattcataaattttgc---agATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
|||| | | | || | | | | | | ||||| | |||| || | | | ||||| | || ||||| ||||||| ||| | ||||||||||| || || |||||||| || ||||||||||||||
-----------------------------------------------------gagtgcgtgttccgagagatttcttcttttctaagaagattttacttCAGATTTTGCGGCAACTAAAGCACGAGAACATTATAGAAATGCTGGATGCATTTGAAAGCCCACAGGAGTTTTGTGTCGTGACAGAATTTGCACAG
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ33693 (Selaginella moellendorffii), 3'ss of exon 2
atttattattgttgctgctaattattataattattaatttattaattacttataagtgtttctgctgactagtgacatttgaaattcataaattttgcagATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA------
| | |||||| | || | | || || || || ||||| || | | | ||||| | || ||||| ||||||| ||| | ||||||||||| || || |||||||| || ||||||||||||||
--------------------------------------------gtagagtgcgagtgttccgagagatttcttcttttctaagaagattttactt-cagATTTTGCGGCAACTAAAGCACGAGAACATTATAGAAATGCTGGATGCATTTGAAAGCCCACAGGAGTTTTGTGTCGTGACAGAATTTGCACAGGCAAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacttataagtgtttctgctgactagtgacatttgaaattcataaattttgcagATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
tgctgac putative branch site (score: 2)
acatttgaaattcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttattattgttgctgctaattattataattattaatttattaattacttataagtgtttctgctgactagtgacatttgaaattcataaattttgcagATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - -ttgctgc