Sequence
atgc intronic sequence ATGC exonic sequence...acacacacgttcaacaaaatttacacaactattattataattattatttctttttctaagctttagcaaacttatggtatcagtcagtttttgacttcagGTGCTCACTTACTCTGCTACCCTGGGGCATTTAACATGACAACTAGACCATTACATTGGGAGTTATT
Basic information
species | Glycine max |
transcript | GLYMA20G02020.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G12040.2 (Arabidopsis thaliana), 3'ss of exon 5
----acacacacgttcaacaaaatttacacaactattattataattattatttctttttc--------taagctttagcaaactt-atggt--atcagtcagtttt--tgacttcagGTGCTCACTTACTCTGCTACCCTGGGGCATTTAACATGACAACTAGACCATTACATTGGGAGTTATT------------
|| | || | |||| ||| | | ||| | | |||||||| || | |||| ||| | || | || ||| | | ||||| ||||| || || |||||||| || || ||||||||||||||| ||||||| |||||||| ||| |
gtgagtcttcatat-cataatgctttatccaaatgg-actatctgcttcctctctttttcgggtccattacgttttaaagaacctcatcacccacatgtttactttaatcatatcagGGGCTCATTTGCTGTGCTACCCGGGAGCCTTTAACATGACAACTGGACCATTGCATTGGGAATTACTACAAAGGGCCAG
upper sequence: GLYMA20G02020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01690.t01 (Vitis vinifera), 3'ss of exon 5
------acacacacgttcaacaaaatttacacaactattattataattattatttctttttctaagctttagcaa-acttatggtatcagtcagtttttgacttcagGTGCTCACTTACTCTGCTACCCTGGGGCATTTAACATGACAACTAGACCATTACATTGGGAGTTATT------------
| | | ||| || ||| ||| | | || || || |||| || |||| |||| | | | ||||| | ||||||| || ||||| |||||| | | ||||| |||||||||||||||||||||||| ||||||| ||||||||||||||
ctcgccatttatttacttgtcaac-ttgacatcactctattaatcatgat--tttcacgttataagttttactgagagtaatggt----gccagttttcaacatcagGCGCTCACCTGATTTGCTATCCTGGGGCATTTAACATGACAACTGGACCATTGCATTGGGAGTTATTGCAAAGGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctttttctaagctttagcaaacttatggtatcagtcagtttttgacttcagGTGCTCACTTACTCTGCTACCCTGGGGCATTTAACATGACAACTAGACCATTACATTGGGAGTTATT
ttttgac putative branch site (score: 3)
ttttt CT-rich tract
tttttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acacacacgttcaacaaaatttacacaactattattataattattatttctttttctaagctttagcaaacttatggtatcagtcagtttttgacttcagGTGCTCACTTACTCTGCTACCCTGGGGCATTTAACATGACAACTAGACCATTACATTGGGAGTTATT
acacaca
- - - - - - aacaaaa
- - - - - - - - - - - acacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttatgg