Sequence
atgc intronic sequence ATGC exonic sequence...aattgcataattttttttatataaaggataatattttggtgcctagaactatagattttcctttttcttattgtttggatggatatgcttattaatatagGGCTTCACATACCCCGTTAGAACTCACTTTTTGGAGAACATTCTTGAAATGACGGGCTACAGATTAACTCCTTATAATCAAATCGATGATTATGGTCAAG
Basic information
species | Glycine max |
transcript | GLYMA20G25800.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 2
aattgcataattttttttatataaaggataatattttggtgcctagaactatagattttccttt-ttcttattgtttggatggat---atgcttattaatatagGGCTTCACATACCCCGTTAGAACTCACTTTTTGGAGAACATTCTTGAAATGACGGGCTACAGATTAACTCCTTATAATCAAATCGATGATTATGGTCAAG
|| || || || ||| | ||| || | | |||||| | || || ||| || || | || | | || | | | | | |||| ||||| || || ||| | | || ||| | || | ||||| ||||| || || |||||||||||||||| |||||||| ||||| ||||||||||
-atca-gtagggttattcataagagagatcctaacctag--cctagattaaagcatcttattttattaggatggccctcattggttgcatacatctcatttcagGGTTTCACTTATCCTGTTCGGAGTCGATTTCTAGAAGATATTCTCGAAATTACTGGGCACAGATTAACTCCTTACAATCAAATTGATGACTATGGTCAAG
upper sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------aattgcataattttttttatataaaggataatattttggtgcctagaactatagattttcctttttcttattgtttggatggatatg---cttattaatatagGGCTTCACATACCCCGTTAGAACTCACTTTTTGGAGAACATTCTTGAAATGACGGGCTACAGATTAACTCCTTATAATCAAATCGATGATTATGGTCAAG
|| || | ||| || | | | | | | | | || ||||| | | || | | || | |||| | | | ||||||| || ||||| || ||| | | ||| || | ||| | ||||| || ||||| | |||||||| ||||| || |||||||| ||||||||||||||||
gtaagtaagaaacatatttgtttatcctctttagaacatttcaagatatttaatcttttgctgagttcaatattccttggatctatatgctctgattaaccccagtgaaactactaatattgtcttcttcactatagGGATTTACATATCCAGTTCGTAGTCATTTCCTAGAGGATATTCTGGAGATGACCCGGTACAGATTGACTCCATACAATCAAATTGATGATTATGGTCAAG
upper sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 8
-aattgcataattttttttatataaaggataatattttggtgcctagaactatagattttcctttttcttattgtttggatggatatgcttattaatatagGGCTTCACATACCCCGTTAGAACTCACTTTTTGGAGAACATTCTTGAAATGACGGGCTACAGATTAACTCCTTATAATCAAATCGATGATTATGGTCAAG
| ||| | | ||| | | ||||| | | | || | || | | |||| | || || | || | | | || ||||| || |||||||| ||||||| | || |||| || ||||| |||||||| || |||||||| ||||| || |||||| | |||||||||||||| |
cagttggaaattttagtcagagtggaggatgaaaactcc-catgtaatggtggagctcatgtcttttttattttatttttttaatgttttctgtgatgtagGGTTTTACATACCCAATTAGAACGTATTTCCTGGAAAATATTCTGGAAATGACAGGATACAGATTGACTCCGTACAATCAAGTTGATGATTATGGTCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaactatagattttcctttttcttattgtttggatggatatgcttattaatatagGGCTTCACATACCCCGTTAGAACTCACTTTTTGGAGAACATTCTTGAAATGACGGGCTACAGATTAACTCCTTATAATCAAATCGATGATTATGGTCAAG
tattaat putative branch site (score: 2)
atatgcttattaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattgcataattttttttatataaaggataatattttggtgcctagaactatagattttcctttttcttattgtttggatggatatgcttattaatatagGGCTTCACATACCCCGTTAGAACTCACTTTTTGGAGAACATTCTTGAAATGACGGGCTACAGATTAACTCCTTATAATCAAATCGATGATTATGGTCAAG
- -tgcataa
- - - - - - - - - - - - - - - - - - tggtgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatatgc