Sequence
atgc intronic sequence ATGC exonic sequencegtaagacagtagtagatcatgattttcttaatattgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC
Basic information
species | Glycine max |
transcript | GLYMA06G11540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
-----------------gtaagacagtagtagatc--atgattttcttaatattgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC
||| | | || ||| | ||| ||| || ||||| | ||||| | | | ||| ||||| |||||||| |||||||| ||||||||||| || ||||| |||||||| || || ||||| || || ||||| |||||||| || |||||||||
gtacgtacctgcagctactaaagccactgaagtctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatg-tgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagacagtagtagatcatgattttcttaat------attgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC
|||| | || | || | |||||||| || || | ||| || || || ||| || || || ||| || ||||| || || || ||||| |||||||||| || ||||| ||||| |||||||| |||||||||||||| || || || ||||| ||||||||
gtaaattaataatcaatgttcattttctttattatatggttttttcatattgaaaattaattaatataaaaaatgatttgcagCAATATATATTATATTAATGACAAATTGGACAAGAGGACATGGACATACATATTTGGGGCGTGCTGTGCAACAACTGTTTTTATTCCTTCCTTCCACAAT
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------gtaagacagt---agtagatcatgattttcttaatattgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC
|| | || ||| | | | | ||| | | || | | || | || |||| | | ||| ||||| ||||||||||| |||||| | ||||||||||||||||| |||||||| || || |||||||| || || || ||||| ||||| ||||| ||
gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttccattgatat-gctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcttaatattgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC
tcttaat putative branch site (score: 3)
ttgtttc putative PPT
attataaactaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacagtagtagatcatgattttcttaatattgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG