Sequence
atgc intronic sequence ATGC exonic sequence...ttttgaagtaattaagtgattattaattcatggaaactatatactagttgtagtgttttctggctgcttttatcatttttatgtttgggttgatgagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAAACGAAATTTGTTCTTGCAAAGGCCTTGA
Basic information
species | Glycine max |
transcript | GLYMA06G43820.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 2
ttttgaagtaattaagtgattattaattcatggaaactatatactagttgtagtgttttctggctgcttttatcatttttatgtttgggttgatgagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAAACGAAATTTGTTCTTGCAAAGGCCTTGA
| || || | | | ||| | || | ||| | | || || | ||| | | | | |||||| | |||| ||| ||||||| || |||||||| ||||| || ||||| | ||||||||||||||||| || || || | |||||||| |||||||| ||| |||| || ||||
gtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatata--caatatgatcattaccaaatttg--ttg-----cagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCTGGAGAGGGACCTTTAGCACAAACTAAATTTGTGCTTTCAAAAGCTTTGA
upper sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------------------------ttttgaagtaattaag--tgattattaattcatggaaactata----tactagttgtagtgttttctggctgcttttatcatttttatgtttgggttgatgagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAAACGAAATTTGTTCTTGCAAAGGCCTTGA
|| ||||| | || | | | | | || | || | || ||||| | ||| ||| | | | || ||| | |||| |||||||| || || |||||||||||||| ||||| || || |||||||||||||| ||||| || |||||||| || || ||||||||||| || |||||||
gtatgatactgatcttacttttagcgtattatttgattctcatgctcgtttttagtagaaatgcatattagtggacaaaagataaattaattagaagttctcaatacctactcatggtctgttgacattaggatactccttactgtagaacataggtgctatctttgtgactattttgtgtat-ttgaattatagGTTGAACGAGTCGTTGGTATGGTTGAAGGAGCTATATTAGTTGTTGATGCTGGAGAAGGCCCTCTTGCACAGACTAAGTTTGTTCTTGCCAAAGCCTTGA
upper sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G31060.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------------------------------------------ttttgaagtaattaag--tgattattaattcatggaaactata----tactagttgtagtgttttctggctgcttttatcatttttatgtttgggttgatgagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAAACGAAATTTGTTCTTGCAAAGGCCTTGA
|| ||||| | || | | | | | || | || | || ||||| | ||| ||| | | | || ||| | |||| |||||||| || || |||||||||||||| ||||| || || |||||||||||||| ||||| || |||||||| || || ||||||||||| || |||||||
gtgaggtatgatactgatcttacttttagcgtattatttgattctcatgctcgtttttagtagaaatgcatattagtggacaaaagataaattaattagaagttctcaatacctactcatggtctgttgacattaggatactccttactgtagaacataggtgctatctttgtgactattttgtgtat-ttgaattatagGTTGAACGAGTCGTTGGTATGGTTGAAGGAGCTATATTAGTTGTTGATGCTGGAGAAGGCCCTCTTGCACAGACTAAGTTTGTTCTTGCCAAAGCCTTGA
upper sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 2
ttttgaagtaattaagtgattattaattcatggaaactatatactagttgtagtgttttctggctgcttttatcatttt-ta--tgtttgggttgatgagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAAACGAAATTTGTTCTTGCAAAGGCCTTGA
|| | ||| | | | || || || | | | | || | || | | || || ||| || | || | || || || ||||||||||| |||||||| |||||||| ||||| |||| ||||| ||||||||||||||||| ||||||||||| || ||||| |||||||| ||||| |
-ggtgtaagctttacttacacactggtt--tgcaagttttcttgtttttattttgctagatcactaagttgatccttgtataattactttttctgttggttagGTTGAGCGGGTTGTTGGCATGGTTGAAGGAGCAGTTTTAGTTGTAGATGCTGGTGAAGGTCCCCTTGCACAAACAAAGTTTGTCCTTGCAAAAGCCTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgtagtgttttctggctgcttttatcatttttatgtttgggttgatgagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAAACGAAATTTGTTCTTGCAAAGGCCTTGA
ggttgat putative branch site (score: 5)
ttttatcatttttatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgaagtaattaagtgattattaattcatggaaactatatactagttgtagtgttttctggctgcttttatcatttttatgtttgggttgatgagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAAACGAAATTTGTTCTTGCAAAGGCCTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG