Sequence
atgc intronic sequence ATGC exonic sequence...aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctagtgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT
Basic information
species | Glycine max |
transcript | GLYMA18G07480.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctag----tgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT-
|| | | ||| || | | | ||||| || ||| |||| | ||||| || || | | | ||||| || |||||||| || ||||||||||| | |||||||| || ||||||||| ||||||| ||||||||||| ||||||||| ||||||| ||||||
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
-aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctagtgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT-
||| ||| | | | || ||| | | | || | ||| || | | | | | || | ||| |||| || ||||| || |||||||| ||||| ||||| || | ||||||||||| ||||||||| ||||||| ||||||||| | ||||||||| ||||||| |||||
caaggattcatggcatctgagttttactttccaattgggattt-cataaatttccataattttccaatgatgcaaattaatatttaacg-attttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 3
aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctagtgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT-
|||||| |||| ||||| | | || | |||| | ||| ||||| | |||| || | | | || ||| ||||||| |||||||| |||||||||||||| | || || ||||| || || || ||||||| ||||| || || ||| ||||| ||||||| ||||||
gtacatttt----aagttaccatttttctctttgaagacttggg------acctaa---ataaa--ttattttttgatctctc---catgtttgcttgtagGAGAAAGATGCAGCTCTAGGAAATGGTGGGTTAGGGAGACTTGCCTCGTGTTTCTTGGATTCGATGGCCACCCTAAATCTGCCTGCTTGGGGTTATGGTT
upper sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 2
---aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctagtgtataaaactca--tttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT-
||||| | | | || ||| || | ||| | | | | | || | | | | |||| || | || | | || | || |||| || ||||| ||||||||||||||||| || || ||||||||||| |||||||| || |||||||||||| | ||||||||| | ||||| ||||||
agtctgcattcttcgattgta---gtttatttgaaataatgat--atctctgcgtttggtctcaacttttgaactttgatg-attataagaaatgatatcttatagGAAAAAGATGCGGCACTAGGAAATGGTGGACTGGGAAGGCTTGCTTCATGCTTTCTTGACTCCATGGCAACATTAAATTTGCCTGCGTGGGGATATGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatatctagtgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT
ttttaat putative branch site (score: 3)
tataaaactcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctagtgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT
- - - - - - - - - -gcatttc
- - - - - - - - - - - - - - catatgt
- - - - - - - - - - - - - - - - - - tggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattaa