Sequence
atgc intronic sequence ATGC exonic sequencegttagtttctgattacaatggctttatgctccattttatgtagcgtccaatacattggttcgatctctttacatgcttttcaaattaatgtttattttcatacacacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCTTTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA
Basic information
species | Glycine max |
transcript | GLYMA04G00640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
gttagtttctgattacaatggctttatgctccattttatgtagcgtccaatacattggttcgatctctttacatgcttttcaaattaatgtttattttcatacacacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCTTTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA
||| | | | ||| | ||||| || | | || | || || | || | ||| ||| |||| ||| | |||||||||||| |||||||| || ||||||||||| |||||||||||||| ||||| ||||| | ||| || || || ||||| |||||| |||| ||||||
------gtctcaccatgaaaaattt----tgtattttgagttgagaaaaaatgaaaaaaaggaactttagtcacccacttc--atttgggtttggttt---------gtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 1
gttagtttctgattacaatggctttatgctccattttatgtagcgtccaatacattggttcgatctctttacatgcttttcaaattaatgtttattttcatacacacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCTTTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA
| || | | | ||| | |||| | | || | | ||| | | | || | ||| | | |||| || | | | |||||||||||||| ||||| ||| |||||||||| || || ||||||||| | || |||| | | || || ||||||| ||| |||| || | |||||
-----gtgaggacaaacagagttttgggacttttttttttcttcctcttcttcgttgttgtgctt-------gtgatcttcgcctcacggttt-cttctgtggtgat-ttccagGTGGCTCAAGTGCTGCTCACGCTGCCATACTCCTTCTCGCAGCTGGGATTCGCGTCGGGCATTGTCTTCCAGATCTTCTATGGCCTGCTCGGGGCCTGGA
upper sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 1
gttagtttctgattacaatggctttatgctccattttatgtagcgtccaatacattggttcgatctctttacatgcttttcaaattaatgtttattttcatacacacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCTTTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA
| ||| | ||| | |||| | | ||| | | | | | | | | || || | ||| | | |||| || | | | |||||||||||||| ||||| ||| |||||||||| || || ||||||||| | || |||| | | || || ||||||| ||| |||| || | |||||
-------gacaaacaca-cagttttgggacttttttttttcttcttcctcttcttcg--ttgttgtgcttg--tgatcttcgcctcacggttt-cttctgtggtgat-ttccagGTGGCTCAAGTGCTGCTCACGCTGCCATACTCCTTCTCGCAGCTGGGATTCGCGTCGGGCATTGTCTTCCAGGTCTTCTATGGCCTGCTCGGGGCCTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgatctctttacatgcttttcaaattaatgtttattttcatacacacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCTTTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA
aattaat putative branch site (score: 3)
ttttcaaattaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttctgattacaatggctttatgctccattttatgtagcgtccaatacattggttcgatctctttacatgcttttcaaattaatgtttattttcatacacacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCTTTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA