Sequence
atgc intronic sequence ATGC exonic sequence...aatatttgtttttagttcagatactaagagttcttcacatcattccatctttgttggcgtgtctcctttagcttacacatacagcttttcaaattgacagGGTGTGAATGTCGATGATCTTGAGACAAATCATATTGTCCTTGTTCACGGAGGTGGCTTCGGGGCCTGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
Basic information
species | Glycine max |
transcript | GLYMA18G50420.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G50420.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G29770.1 (Arabidopsis thaliana), 3'ss of exon 1
aatatttgtttttagttcagatactaagagttcttcacatcattccatctttgttggcgtgtctcctttagcttacacatacagctttt-----caaattgacagGGTGTGAATGTCGATGATCTTGAGACAAATCATATTGTCCTTGTTCACGGAGGTGGCTTCGGGGCCTGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
|| |||| | | || | || | | | | | |||| || ||| | | | || | |||| | |||| | | ||||| | || | ||||| | || ||||| ||| ||||||||||||| |||||| | || || || ||||||||||| ||| |||| |||||||| || |
--gatccattttgggataggaaa--aaaattggattata-cattttattggagttcatattttttctcgaacttaaattctttttttttactgatatttgagtagGGTATAAAGCTAGATGACTTGGAAACAAACCATTTTGTCCTTGTTCATGGAGGTAGTTTTGGCGCTTGGTGTTGGTATAAAACCATTGCACTTCTTGAGG
upper sequence: GLYMA18G50420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0068g00390.t01 (Vitis vinifera), 3'ss of exon 1
-aatatttgtttttagttcagatactaagagttcttcacatcattccatctttgttggcgtgtctcctttagcttacacatacagcttttcaaattgacagGGTGTGAATGTCGATGATCTTGAGACAAATCATATTGTCCTTGTTCACGGAGGTGGCTTCGGGGCCTGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
||||| | | || | || ||| || | | || || || | | | || | || ||| | |||||||| |||||| | |||||||| ||||| || ||| |||||||||| || |||||||| || || || ||||||||||| ||| | ||||| ||||||||||
caatatgtttattgctattgaatccta-gaatgtaaaatatttttttttcgtaagtcattctcattgttgcaccgtttttaactattttcctctttgacagGATGTGAAGCTTGATGATCTAGAGACCAACCATTTTGTCCTTGTCCATGGAGGTGGTTTTGGTGCTTGGTGTTGGTATAAAACTATAGCGCTTCTAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctttgttggcgtgtctcctttagcttacacatacagcttttcaaattgacagGGTGTGAATGTCGATGATCTTGAGACAAATCATATTGTCCTTGTTCACGGAGGTGGCTTCGGGGCCTGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
agcttac putative branch site (score: 3)
cttttca putative PPT
ttttcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatatttgtttttagttcagatactaagagttcttcacatcattccatctttgttggcgtgtctcctttagcttacacatacagcttttcaaattgacagGGTGTGAATGTCGATGATCTTGAGACAAATCATATTGTCCTTGTTCACGGAGGTGGCTTCGGGGCCTGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
- - - - - - - - - - - - - - - - - -cacatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcgtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatac