Sequence
atgc intronic sequence ATGC exonic sequencegtatagcttcttttggttgctgctatatattgtcattgatttgcatgattttaattaatcttagctaagattgtaactatatctctgtagGGAATGAGTTTCACAACTGACAAGTTGAGGTCATTGGTGCGAAAATGGCAAACTTTAATTGAAGCTCATGCTGATGTGAAGACCACTGATAATTATACTT
Basic information
species | Glycine max |
transcript | GLYMA06G11940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11940.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g21798.1 (Oryza sativa), 3'ss of exon 3
gtatagcttcttttggttgctgctatatattgtcattgatttgcatgattttaattaatcttagctaagattgtaactatatctctgtagGGAATGAGTTTCACAACTGACAAGTTGAGGTCATTGGTGCGAAAATGGCAAACTTTAATTGAAGCTCATGCTGATGTGAAGACCACTGATAATTATACTT
||| |||||| || | ||| | || || ||| | ||||| || ||| | | ||||| ||||||| ||||||||||| || |||||| | || |||||||| |||||||| || |||| || ||||||| ||||| |||||||||||||| || |
gtaatgcttctcttactg--tgcaaaattacttctccaggttgta--atttttgttg---ttaaccag--ttgta---------ttgtagGGCATGAGTTTCACGACCGACAAGCTCAGATCATTGGTCAAGAAATGGCAGACGCTAATAGAGGCTCATGTGGATGTAAAGACCACTGATAACTACATGC
upper sequence: GLYMA06G11940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34670.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatagcttcttttggttgctgctatatattg-tcattgatttgcatgattttaattaatcttagctaagattgtaactat---atctctgtagGGAATGAGTTTCACAACTGACAAGTTGAGGTCATTGGTGCGAAAATGGCAAACTTTAATTGAAGCTCATGCTGATGTGAAGACCACTGATAATTATACTT
| | ||| | || | ||| | || | ||| || | | || | | | | |||||||||||| ||| ||||||||| |||||| | |||||||||||| || ||||| ||||| |||||||| |||| |||||||| ||||| || || || |
---------------------gtaagataaagaccactcctttac-tggcat--attgatacagagtgcggtttttaatctgtgatctctgtagGGTATGGATTTCACAACCGACAAGCTAAGGTCATTGGTGAAGAAGTGGCAGACTTTGATTGAAGCCCATGTCGATGTGAAAACCACAGACGGCTACACCT
upper sequence: GLYMA06G11940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g03900.t01 (Vitis vinifera), 3'ss of exon 4
------------------------gtatagcttcttttggt-tgctgctata--tattgtcattgatttgcatgattttaattaatcttagctaagat-tgtaactatatctct--------gtagGGAATGAGTTTCACAACTGACAAGTTGAGGTCATTGGTGCGAAAATGGCAAACTTTAATTGAAGCTCATGCTGATGTGAAGACCACTGATAATTATACTT
|| | ||| || | | | ||| |||| | ||| | | ||| |||| ||| | || || || | | || | || | |||||||| ||| |||||||||||||||||||| |||||||| ||||||||||| || ||||||||||||| ||||||||||| ||||| || || || |
gtatgacagagatcctgaggtcctataaattttcattctatgtaatcttatgattatttttatttttatttatgtatttatttattttttaacaaaatgtttttcttttccttttggaaaatacagGGAATGGATTTTACAACTGACAAGTTGAGGTCTTTGGTGCGGAAATGGCAAACATTGATTGAAGCTCATGTGGATGTGAAGACAACTGACAACTACACCT
upper sequence: GLYMA06G11940.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S46_147V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------gtatagcttcttttggttgctgctatatattgtcattgatttgcatgattttaattaatcttagctaagattgtaactatatctctgtagGGAATGAGTTTCACAACTGACAAGTTGAGGTCATTGGTGCGAAAATGGCAAACTTTAATTGAAGCTCATGCTGATGTGAAGACCACTGATAATTATACTT
| | ||| | |||| || | | | | | |||| | ||| |||| | | | | | || || |||||||| ||||||| |||||| || |||| |||| || || ||||| | |||||| |||||||| | |||||||||||||||||| || ||
gacgaagtcatggtattgggagagcagtggtacgttgttgatgttggctaaaggtaagg-gcatcgtgttacttaac---ggatcgacctttgattaaattc----agGGAATGGACCTCACAACCGACAAGCTGCGGTCTCTGGTTCGCAAGTGGCAGAGTTTAATCGAAGCTCACGTTGATGTGAAGACCACTGACAACTACCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatttgcatgattttaattaatcttagctaagattgtaactatatctctgtagGGAATGAGTTTCACAACTGACAAGTTGAGGTCATTGGTGCGAAAATGGCAAACTTTAATTGAAGCTCATGCTGATGTGAAGACCACTGATAATTATACTT
ttgtaac putative branch site (score: 2)
tatctct putative PPT
attttaattaatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagcttcttttggttgctgctatatattgtcattgatttgcatgattttaattaatcttagctaagattgtaactatatctctgtagGGAATGAGTTTCACAACTGACAAGTTGAGGTCATTGGTGCGAAAATGGCAAACTTTAATTGAAGCTCATGCTGATGTGAAGACCACTGATAATTATACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA