Sequence
atgc intronic sequence ATGC exonic sequence...ttcatatgattgttgttttgcaagaagtctttataagtttgttcgttatctgttctatctgtctctgtatagtcttgatgttctagttttctatgtccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGCGGTGCTTTG
Basic information
species | Glycine max |
transcript | GLYMA17G05000.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05000.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 2
-ttcatatgattgttgttttgcaagaagtctttataagtttgttcgttatc-tgttctatctgt-ctctgtatagtcttgatgttctagttttctatgtccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGCGGTGCTTTG
|| || || ||| | | | || | | || | | || || | | ||| || ||| | || || | ||| | ||| ||||| | || || ||||||||||| ||||| |||||||| ||||||||||| ||| | || | || || ||||| | || || ||||| ||||| |
ttttatcaagttattggcctttgaaa---tttcacactttattactttttcgtatcttattagtgctccatgtaagagcttcattttggttctttatttccagTTTTGTTGTAAAAGGAGTTGTTTGTAAGAAGAATGTTGCTCATCGGCGCATGGCGTCACGGAAAGAAAAGCCACGCATCCTGATCCTTGGTGGTGCACTT
upper sequence: GLYMA17G05000.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 3
-ttcatatgattgttgt---tttgcaagaagtctttataagtttgttcgttatctgttctat-ctgtctctgt-atagtcttgatgttctagttttctatgtccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGCGGTGCTTTG
||||| | ||||||| | | | || |||||| | ||| || ||| | | |||| | | || | || | || |||| || | ||||| || ||||||||||| ||||| || ||||||||||||||||||||||| |||| || || || || ||| | ||||| ||||| || ||| ||
cttcatgtttttgttgtgaatattccgtgaggatttatatctctgtcgattggctggtaaacactgtattactgattgaactgggatggtattttttta------gTATGGTCGTGAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGGCGAATGACTTCAAAGATCGAGAAGCCGCGTCTGCTAATCCTTGGAGGAGCTCTG
upper sequence: GLYMA17G05000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g00360.t01 (Vitis vinifera), 3'ss of exon 2
ttcatatgattgttgttttgcaagaagtctttataagtttgttcgttatctgttctatctgtctctgtatagtcttgatgttctagttttctatgt-ccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGCGGTGCTTTG
|| ||| | |||||| | | | || || | | | | ||| | ||| | || | ||| || || ||| ||| | |||| |||||||||||||||||||| ||||| || |||||||||||||| ||||||||| | ||||| |||||||||||| ||| | || || || ||| ||
-acaattgacaatcaccttgcaaacactttaactagaggatgctgtcaatttctttttctttttctttgtactgatgaaattttaatttcatatcttccagTATGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCATCGACGAATGACATCTAAAATAAGTAAACCACGTTTCCTACTCCTCGGAGGAGCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatctgttctatctgtctctgtatagtcttgatgttctagttttctatgtccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGCGGTGCTTTG
tcttgat putative branch site (score: 4)
ttttctat putative PPT
ttttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcatatgattgttgttttgcaagaagtctttataagtttgttcgttatctgttctatctgtctctgtatagtcttgatgttctagttttctatgtccagCATGGTGGTTAAAGGAGTTGTATGTAAAAAGAATGTGGCTCATCGGCGAATGACAGCAAAAATTGATAAACCACGTTTTCTAATACTTGGCGGTGCTTTG
- - - - - tgttgtt
- - - - - - - - - tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgatg