Sequence
atgc intronic sequence ATGC exonic sequence...tttttcggggtggaggtagggggtttgcatcttactctgtatatgtcaatcttttatatcataatgccgtccaagaaaatgacttgattttcattctcagAGATGGACCGGAGTGTGAAGCGAATGTTGAAGCTGATAGAAGAGGATGCAGATTCATTTGCCAAAAAAGCTGAAATGTATTATCAGAAGAGGCCAGAATT
Basic information
species | Glycine max |
transcript | GLYMA02G40300.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G40300.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G58320.3 (Arabidopsis thaliana), 3'ss of exon 1
------------------------tttttcggggtggaggtag------ggggtttgcatcttactctgtatatg-tcaatcttttat---------atcataatgccgtccaagaaaatgacttg----attttcattctcagAGATGGACCGGAGTGTGAAGCGAATGTTGAAGCTGATAGAAGAGGATGCAGATTCATTTGCCAAAAAAGCTGAAATGTATTATCAGAAGAGGCCAGAATT
||| | || | || || || | | | | || || | | |||||| | | | || ||||| ||| ||| || | || ||||||||||||||||| ||||| || ||| ||||| ||||||| |||||||||||||| ||||| || || || || |||||||| ||| || || || |
gtgagtccattcacattatgtcgttttcatgtaatgaaaataccttattaggcttagggtttcccaaattaggtggttagtcttttttcataaaggaaataaaaaatatgccaagtttatgttttgtgtgatgattatgatcagAGATGGACCGGAGCGTGAAACGGATGGTGAAGTTGATAGAGGAGGATGCAGATTCTTTTGCTAAGAAGGCAGAGATGTATTACCAGTCAAGACCTGAGCT
upper sequence: GLYMA02G40300.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g08170.t01 (Vitis vinifera), 3'ss of exon 4
-tttttcggggtggaggtagggggtttgcatcttactctgtatatgtcaatcttttatatcataatgccgtccaagaaaatgacttgattttcattctcagAGATGGACCGGAGTGTGAAGCGAATGTTGAAGCTGATAGAAGAGGATGCAGATTCATTTGCCAAAAAAGCTGAAATGTATTATCAGAAGAGGCCAGAATT
| | || || ||| | | | | | | ||| ||| ||| | | | | | || || | | | | |||||||||||||| ||||||||| || |||||||||||||| |||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| || |||||
ttgtctcattgttgagacaaaataatgttttgccaattaccctgtgtaaat-tttaaaacagtttttgaatagaaactgataaaagggtacttggcctcagAGATGGACCAGAGTGTGAAACGGATGTTGAAGCTGATTGAAGAGGATGGGGATTCATTTGCAAAAAAGGCTGAGATGTATTATCAGAAGAGACCTGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatcttttatatcataatgccgtccaagaaaatgacttgattttcattctcagAGATGGACCGGAGTGTGAAGCGAATGTTGAAGCTGATAGAAGAGGATGCAGATTCATTTGCCAAAAAAGCTGAAATGTATTATCAGAAGAGGCCAGAATT
acttgat putative branch site (score: 5)
ttttcattctc CT-rich tract
ttttatatcataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttcggggtggaggtagggggtttgcatcttactctgtatatgtcaatcttttatatcataatgccgtccaagaaaatgacttgattttcattctcagAGATGGACCGGAGTGTGAAGCGAATGTTGAAGCTGATAGAAGAGGATGCAGATTCATTTGCCAAAAAAGCTGAAATGTATTATCAGAAGAGGCCAGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - -gggtgga
- - - - - - - - - - gggtttg
- - - - - - - - - - - - - - - - - ctctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg