Sequence
atgc intronic sequence ATGC exonic sequence...attaaaaaaacatgtaaaaaatgatttatttattccgagtgttttctttttcaacacttccatcgtagtctcacaatacgtattcgttcttttcttgcagTCCAGACGCCACACATGGTTTCTACAGGTCTTGAAGATTACAAGGCCAGGGGAACACAAGCGGCTCCTTACTTTATTGTGTCCTTTTACACAGAATTTGC
Basic information
species | Glycine max |
transcript | GLYMA04G34240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G34240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G34050.1 (Arabidopsis thaliana), 3'ss of exon 3
attaaaaaaacatgtaaaaaatgatttattt-attccgagtgttttctttttcaac----acttccatcgtagtctcacaatacgtattcgttcttttcttgcagTCCAGACGCCACACATGGTTTCTACAGGTCTTGAAGATTACAAGGCCAGGGGAACACAAGCGGCTCCTTACTTTATTGTGTCCTTTTACACAGAATTTGC
| ||| ||| ||| | || ||| | | ||| | | || | | ||| | ||| | | | | ||| | || | ||||| | |||| |||||| ||| ||| ||||| ||||| ||||| || || ||||| ||||||||||||||| | | | |||| ||||| || || |
-----tgtaccatttaattcatgttgagcttcattacaacagttatgtaactcggctgaagagttcattatgatcttatataaatggtcagttttattgtggcagTTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAGGAACTCAAGCGGCTCCTTACCTGACTACAACCTTCTACACTGAGCTTTC
upper sequence: GLYMA04G34240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g00660.t01 (Vitis vinifera), 3'ss of exon 3
-----------attaaaaaaacatgtaaaaaatgatttatttattccgagtgttttctttttca-acacttccatcgtagtctcacaatacgtattcgttcttttcttgcagTCCAGACGCCACACATGGTTTCTACAGGTCTTGAAGATTACAAGGCCAGGGGAACACAAGCGGCTCCTTACTTTATTGTGTCCTTTTACACAGAATTTGC
|| | | ||| || | ||| || | || | | | | |||| | || | | ||| || || |||||| || | || ||||||| ||| || |||||||||||||||||||| || ||||| ||||| ||||| ||||| | ||| | ||||||||||| |||||
tctcctccttaatcagtagtgtttgtggaactgaa---gcttaggatgaataccttagtatgaatatttgtccactgaagcttt--------tgttcaag-ttgtcatgcagTTCAAATGCAACACATGATTTTCACTGGTCTTGAAGATTACAAGGCAAGAGGAACTCAAGCAGCTCCCTACTTCACTGTCACTTTTTACACAGACTTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttcaacacttccatcgtagtctcacaatacgtattcgttcttttcttgcagTCCAGACGCCACACATGGTTTCTACAGGTCTTGAAGATTACAAGGCCAGGGGAACACAAGCGGCTCCTTACTTTATTGTGTCCTTTTACACAGAATTTGC
gtctcac putative branch site (score: 3)
tattcgttcttttctt putative PPT
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaaaaaaacatgtaaaaaatgatttatttattccgagtgttttctttttcaacacttccatcgtagtctcacaatacgtattcgttcttttcttgcagTCCAGACGCCACACATGGTTTCTACAGGTCTTGAAGATTACAAGGCCAGGGGAACACAAGCGGCTCCTTACTTTATTGTGTCCTTTTACACAGAATTTGC
- -aaaaaaa
- - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acttcca