Sequence
atgc intronic sequence ATGC exonic sequence...tggatatttatggaatttatggttctataacaagcatattatctcaattttttttttatatagatattaagtgtgtctataattgattggatctgttcagGTCAAGGATTTGGAAGTAGAACTTGAAACTACCAAACAGAAAAATAAGGAGAACTTGCAGCAGGCTATTCTAATTGAGAGAGAAAGGTTTACTCAAATGC
Basic information
species | Glycine max |
transcript | GLYMA04G06980.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06980.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G25350.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------tggatatttatggaatttatggttctataacaagcatattatctcaattttttttttatatagatattaagtgtgtctataattgattggatctgttcagGTCAAGGATTTGGAAGTAGAACTTGAAACTACCAAACAGAAAAATAAGGAGAACTTGCAGCAGGCTATTCTAATTGAGAGAGAAAGGTTTACTCAAATGC
| ||| || |||| | || || | || ||| | || || || | | | ||| | ||| || |||||||||| | ||| ||||||| |||||||||||||| ||||||| ||| || ||||| ||| |||| ||| | | | |||||| | || |||| | ||||
gtacatgattgaaaataatagtacatctgttttcaagtttgttggtaatgaaatctgcgcttcttcc---tttactcttcatgcgaatgtcatatatgt--aatcttggtttt-cctgttcagGTTGATGATCTGGAAGTGGAACTTGAAACTACTAAACAGAGAAACAAAGAGAATTTGGAGCAAGCTTTGATGACCGAGAGACAGAGTGTTACCAAGATGC
upper sequence: GLYMA04G06980.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g05630.t01 (Vitis vinifera), 3'ss of exon 6
tggatatttatggaatttatggttctataacaagcatattatctcaattttttttttatatagatatta-agtgtgtctataattgattggatctgttcagGTCAAGGATTTGGAAGTAGAACTTGAAACTACCAAACAGAAAAATAAGGAGAACTTGCAGCAGGCTATTCTAATTGAGAGAGAAAGGTTTACTCAAATGC
| | ||||| | || | | ||| || || | | ||||| ||| ||| || | | | || | |||| | | ||||||||| ||||||||||| |||||||||||||| ||||| |||| ||| || ||| ||||||| ||||| ||||||| |||||||| | ||||||||||
-gattctttatcgttacaatcttctgctgacagattctgtaaaaaccttaatactatatatggatgttatagactatatctagctaattgtaacatctcagGTCAAAGATTTGGAAGTGGAACTTGAAACTACGAAACAAAAAAGTAAAGAAAACCTGCAGCAATCTATTTTAATTGAAAGAGAAAGAGTCACTCAAATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttttttttatatagatattaagtgtgtctataattgattggatctgttcagGTCAAGGATTTGGAAGTAGAACTTGAAACTACCAAACAGAAAAATAAGGAGAACTTGCAGCAGGCTATTCTAATTGAGAGAGAAAGGTTTACTCAAATGC
aattgat putative branch site (score: 4)
tctgttc putative PPT
tttttttatatagata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggatatttatggaatttatggttctataacaagcatattatctcaattttttttttatatagatattaagtgtgtctataattgattggatctgttcagGTCAAGGATTTGGAAGTAGAACTTGAAACTACCAAACAGAAAAATAAGGAGAACTTGCAGCAGGCTATTCTAATTGAGAGAGAAAGGTTTACTCAAATGC
- - - - - - - - - - - - - - - caagcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtc