Sequence
atgc intronic sequence ATGC exonic sequencegttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
Basic information
| species | Glycine max |
| transcript | GLYMA18G00430.2 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g28990.1 (Oryza sativa), 3'ss of exon 5
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccgg-attttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
||| | || | || ||| | ||| || | | ||| ||||| |||| || ||||| | || ||||| || ||| | | | ||| | || |||| || || | ||||||||| | ||||||||||||||||| ||||| ||||| || |||||||
gtttcacttcagtgccttggaattccttatttccatttaaacta---caagtaattgtcatttggacta--aatttttcaaacacatttcagGAATCTCTAAGGCGTGTTCTCATTATCTTCTCAAAATTAAATCCTACCATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTCTTTTTTATGTGT
upper sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g30880.1 (Oryza sativa), 3'ss of exon 5
gttcttcctctatttatttttattttcgaat-tcatgccaactcggtcctttttcttgccattttgactt---tcaacttttccggat-----tttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
| |||||| || || | |||||| || | | | | ||| || | | || || | | || | | |||||| | ||||| ||| | | | |||||||| || || |||||||||||||| | ||||| ||||||||||| ||||| || |||| |||||| |
-----------gtaagcatttattatctgatatgatgccagttct-ttttgtcttttgtaatgtccagttaggctaaatgtgatatatgtttgtcttcagGAGTCGCTAAAGCGTATACTTACCATATTTGCAAAATTAAATCCGGGTATAAGATATGTACAAGGAATGAATGAAGTTTTGGCACCACTCTACTATGTTT
upper sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G022308_T02 (Zea mays), 3'ss of exon 6
----gt-tcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
|| | |||| | | | | ||| || || || | || || || | | | ||| | | | || | ||||| | ||||| ||| | | | |||||||| ||||| |||||||||||||| | ||||| |||||||| || ||||| ||||||| ||||| |
gtaggtgtgttccctgacatgggatcactttttttttgttgtcagtaacattgttcagttt----ttctaa--tgcaatatgttttgtttct--agGAGTCACTAAAGCGTATACTTACAATATTTGCAAAATTGAATCCGGGTATAAGATATGTACAAGGAATGAATGAGGTTTTGGCACCTCTCTATTATGTTT
upper sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
| ||| | | | | | || || || || | | | ||| | |||| |||| | | ||| | ||||| |||| || | || | | | ||||| ||| |||| | || ||||||||| | ||||||||||||||||| ||||| || ||||||| ||| |
-gtaaatctccacgcactctgagttc--aaacagtgttg--tcagatccctgtctgatc-ttttacctttttattattc-----tcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
upper sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G122935_T01 (Zea mays), 3'ss of exon 5
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
||| | || | | || | |||| | | || |||| | | ||| | |||||| || || | | ||||| | || | || || |||||| | ||| |||| |||||| | ||||||||||| | ||||||||||||||||| ||||| ||| | || ||||| |
gtttgtattcagtgt-ttacagtgttcgtactgataccaattg------------taccaatatgacttgattattctctgaccctatcagGAATCCTTGAGGAGAATTTTAATTATATTTTCAAAATTGAACCCCAGTATAAGATATGTGCAAGGGATGAATGAAGTTTTGGCACCTTTATTTTATGTAT
upper sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 5
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactt-tcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
||| | || ||| || | |||| ||| | | | |||||| | | || | | | || ||||| ||||| | || |||||| ||||| |||||||||||||| |||||||||||||| | ||||||||||||||| | ||||| ||||| |||||||| |
---------gtatgtgttgttacttgagg---catga-gacttgatacaaacatcacccatttgaccaaattaaatggatcctgtatttcagGATGCTTTGAGGAACATATTGATTGTGTTTGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
ttttgac putative branch site (score: 3)
tttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
