Sequence
atgc intronic sequence ATGC exonic sequence...accattagagctatgaagaaattttgtttcttgttttcttattgtatctgtcttactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
Basic information
species | Glycine max |
transcript | GLYMA08G13780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 3
accattagagctatgaagaaattttgtttcttgttt--tcttattgtatctgtcttactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
|| | |||| | | || || | |||| | |||| || | | | || || || ||| | | | | || | ||| ||| |||||||| || ||||| ||| |||| ||||||||| | || || ||||| |||| | ||||||| || ||||||||||||||||| || |||
--tgttgggtctattcatgctcccttttaattacatgcccttaaaatttctggtacaccatgctacttattattgttaagtttgaccagtatattttgtcagTCTGATATGACAGGTGTAGTAGTTGATATTGGGGATGGAGCTCCACATGTGGTGCCGGTTGTAAACGGCTACGTAATTGGGAGTAGCATCAAGTCTTTTC
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G305332_T02 (Zea mays), 3'ss of exon 3
accattagagctatgaagaaattttgtttc-ttgttttcttattgtatctgtcttactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
| ||| | || | | || |||| || ||| ||| ||||| || | | | || | || | ||| | | || | ||| ||| ||||||||||| ||||| ||| |||| ||||||||| | || | ||||| |||| | | |||||||| |||||||||||||| || || |||
aaaattgttccaatctcgtgaccttttttcatttaattcctataaattctgtggtagggcac-attgcttctcattaactctggccaatatactttgtcagTCTGATATGACAGGAGTAGTAGTTGATATTGGGGATGGAGCTCCACAAATCGTGCCAGTTGTAAATGGCTATGTAATTGGGAGTAGCATAAAGTCTTTTC
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 2
accat-tagagctatgaagaaattttgtttcttgttttcttattgtatctgtcttactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
| | | | | | | | ||| | || | || || || ||||||| | | | ||| ||| ||| | |||||||||||||||||||||||||| |||||||| |||||||||||||| || ||||| ||||| ||||||||||| || ||||| || ||||| | |||||||||||||
gctttgtgggatttagcaaatattaaacatgttctcttgttttttgttctgtctcgttatgctcgc-ctcgcctcttaatttgacttacaattcttcttagTGTGAGATGACAGGGGTTGTAGTAGATGTTGGAGATGGGGCAACTCATGTTGTACCTGTTGCAGAAGGTTATGTCATCGGGAGCTGTATCAAATCGATTC
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 2
accattagagctatgaagaa-attttgtttcttgttttcttattgtatctgtct------tactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
| | ||| | ||| ||||| | | || | | ||| || | || | | || |||||||| | | || | || ||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||||| ||||||||||| || |||||||||||||| ||||| || || ||||
-------ttgtcttaaagtgtaccttgcttcttatgtaaataatttttcttgctctttgatgattgattgacccttgccttttagattaacctacactttcccttagTGTGAGATGACAGGGGTTGTAGTGGATGTTGGGGATGGGGCTACTCATGTTGTACCTGTTGCAGATGGTTATGTTATTGGGAGCAGCATTAAGTCAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgtcttactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
ttcttctt CT-rich tract
tttaagaatattttcc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accattagagctatgaagaaattttgtttcttgttttcttattgtatctgtcttactttaagaatattttccttttaggctgatctggaattcttcttagTGTGAGATGACAGGAGTTGTAGTGGATGTTGGAGATGGAGCTACTCACGTTGTGCCTGTTGCAGACGGCTATGTTATTGGGAGTAGCATCAAATCGATTC
- - - - - -tatgaag
- - - - - - - - - - - - - - - - - - - - - - - -ctgtctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggctga