Sequence
atgc intronic sequence ATGC exonic sequence...ggctatttatttgcgtaattgttgatatatgttgctggaggactcgcttcatgtttactttcttgtagtttcatataacctattaaccatttcttaatagTTAGTGCTTGTATTCATCACAGAATGGCATCCAACAGGGGTCAAGGTGGAATTCAGCAGTTGTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGC
Basic information
species | Glycine max |
transcript | GLYMA13G20310.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20310.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g47320.1 (Oryza sativa), 3'ss of exon 1
---ggctatttatttgcgtaattgttgatatatgttgctggaggactcgcttcatgtttactttcttgtagtttcatataacct--attaaccatttcttaatagTTAGTGCT-TGTATTCATCACAGAATGGCATCCAACAGGGGTCAAGGTGGAATTCAGCAGTTGTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGC
| ||| | | | | | ||| | |||| | |||||| | | || | ||| | | | | | | | ||| || || | | | |||| | |||| | ||||| | ||||||||||||||||| || |||||||| || ||||| || |||| |||||| |
atatgttatgcaatcacattcat-ttgtgttctgttcatttaggacttgttatat-tccactcggctttcactatgtgttattttgtctaataataaaatagTTCCTCACACCATGTAGCAGAAGGAAGATGGATGCTAACAGACGCCAAGGTGGAATTCAGCAATTATTGGCTGCAGAGCAAGAAGCTCAACAGATTGTTA----
upper sequence: GLYMA13G20310.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G124103_T02 (Zea mays), 3'ss of exon 1
ggctatttatttgcgtaat-tgttgatatatgttgctggaggactcgcttcatgtttactttcttgtagtttcatataacctattaaccatttcttaatagTTAGTGCT-TGTATTCATCACAGAATGGCATCCAACAGGGGTCAAGGTGGAATTCAGCAGTTGTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGC-----------
| || | | ||| ||| |||||| || ||| | | ||| || | | | |||| | |||| ||| | | | | |||| |||||||| | |||||||| |||||||||||| ||||||| || || ||||| || | |||||||||||
-------agctggcattgtgtgtcgatttatgttt-------acacgccttttttttttttgatctgaaacagttgaggtctatct-ctgattctgaattatggattttgcccagGAGCTGAGAGATGGACGCCAACAGGCGCCAAGGTGGGATTCAGCAGTTGCTGGCTGCGGAGCAGGAGGCTCAGCAAATTGTGAATGCGGCTAGAGCTG
upper sequence: GLYMA13G20310.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G124103_T03 (Zea mays), 3'ss of exon 1
ggctatttatttgcgtaat-tgttgatatatgttgctggaggactcgcttcatgtttactttcttgtagtttcatataacctattaaccatttcttaatagTTAGTGCT-TGTATTCATCACAGAATGGCATCCAACAGGGGTCAAGGTGGAATTCAGCAGTTGTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGC-------------
| || | | ||| ||| |||||| || ||| | | ||| || | | | |||| | |||| ||| | | | | |||| |||||||| | |||||||| |||||||||||| ||||||| || || ||||| || | |||||||||||
-------agctggcattgtgtgtcgatttatgttt-------acacgccttttttttttttgatctgaaacagttgaggtctatct-ctgattctgaattatggattttgcccagGAGCTGAGAGATGGACGCCAACAGGCGCCAAGGTGGGATTCAGCAGTTGCTGGCTGCGGAGCAGGAGGCTCAGCAAATTGTGAATGCGGCTAGAGCTGGT
upper sequence: GLYMA13G20310.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G124103_T01 (Zea mays), 3'ss of exon 1
ggctatttatttgcgtaattgttgatatatgttgctggaggactcgcttcatgtttactttcttgtagtttcatataacctattaaccatttcttaatagTTAGTGCT-TGTATTCATCACAGAATGGCATCCAACAGGGGTCAAGGTGGAATTCAGCAGTTGTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGC-----------
||| ||| |||||| || ||| | | ||| || | | | |||| | |||| ||| | | | | |||| |||||||| | |||||||| |||||||||||| ||||||| || || ||||| || | |||||||||||
----------------gtgtgtcgatttatgttt-------acacgccttttttttttttgatctgaaacagttgaggtctatct-ctgattctgaattatggattttgcccagGAGCTGAGAGATGGACGCCAACAGGCGCCAAGGTGGGATTCAGCAGTTGCTGGCTGCGGAGCAGGAGGCTCAGCAAATTGTGAATGCGGCTAGAGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcatgtttactttcttgtagtttcatataacctattaaccatttcttaatagTTAGTGCTTGTATTCATCACAGAATGGCATCCAACAGGGGTCAAGGTGGAATTCAGCAGTTGTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGC
tattaac putative branch site (score: 1)
ccatttctt CT-rich tract
atataacctattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggctatttatttgcgtaattgttgatatatgttgctggaggactcgcttcatgtttactttcttgtagtttcatataacctattaaccatttcttaatagTTAGTGCTTGTATTCATCACAGAATGGCATCCAACAGGGGTCAAGGTGGAATTCAGCAGTTGTTGGCTGCTGAACAAGAGGCACAACGGATTGTGAATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - -tgttgat
- - - - - - - - - - - - - - atgttgc
- - - - - - - - - - - - - - - - - -tggagga
- - - - - - - - - - - - - - - - - - - - - - cgcttca