Sequence
atgc intronic sequence ATGC exonic sequence...tctggcggggctatcagacaccaatataataagtgatttagggatacaaatttgagtgacatgaagaaggctaatttatgtagctggattattgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG
Basic information
species | Glycine max |
transcript | GLYMA14G00520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G00520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
-----tctggcggggctatcagacaccaatataataagtgatttagggatacaaatttgagtgacatgaagaaggctaatttatgtagctggattattgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG
| | || || | || | | ||| | | | ||| | ||| | || | ||| | ||||| | |||||||||||||||| || |||||| |||| ||||| || ||||||||||| || |||||||| | |||||||||||||| | ||
agcattgcagtaatgccatggttctacatttatttggaactcttaagtagttatgttttttttccatattaga---tatatcatgacatctgcttatt--tctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
upper sequence: GLYMA14G00520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 3'ss of exon 4
tctggcggggctatca-gacaccaatataataagtgatttagggatacaaatttgagtgacat-gaagaaggctaatttatgtagctggattat-tgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG
| | | || | ||||||| | | | || | | | | || || || | | | | || | | | || | | |||||| |||||||||| || |||||| | | || ||||| || ||||||||||| | |||||||| || |||||||||||||| | ||
--tatgtgatccattatgacacca-tgttccatgtaactccgtggtagttatgtgtattctgttgttccatatgcataactatgaccatcttctgcttttcagATAATTGATGCTGTTGTTGCTGCACGTATCTTAAATGCCACACTTGTTGTTCCCAAATTGGATCAAACATCTTTCTGGAAAGATGCAAG
upper sequence: GLYMA14G00520.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168614_T02 (Zea mays), 3'ss of exon 4
tctggcggggctatcagacaccaatataataagtga--tttagggat---acaaatttgagtgacatgaagaaggctaatttatgtagctggattattgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG
|| | | ||| | || | | | | | | ||||| | || ||||| || | | | | |||| | | | | | |||||||||||||||| || |||||| | | ||||||||||| ||||||||||| | ||||||| || |||||||||||||| | ||
-cttatgag-ttatttaat-ccgttctgaggactaaagtttagtcactgaacttatttgcttgctttctctatagacgaattataacccctgctgctc--tctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAG
upper sequence: GLYMA14G00520.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168614_T03 (Zea mays), 3'ss of exon 4
tctggcggggctatcagacaccaatataataagtga--tttagggat---acaaatttgagtgacatgaagaaggctaatttatgtagctggattattgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG-----------
|| | | ||| | || | | | | | | ||||| | || ||||| || | | | | |||| | | | | | |||||||||||||||| || |||||| | | ||||||||||| ||||||||||| | ||||||| || |||||||||||||| | ||
-cttatgag-ttatttaat-ccgttctgaggactaaagtttagtcactgaacttatttgcttgctttctctatagacgaattataacccctgctgctc--tctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAGGTATGCGATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaatttgagtgacatgaagaaggctaatttatgtagctggattattgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG
tattgat putative branch site (score: 3)
taatttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctggcggggctatcagacaccaatataataagtgatttagggatacaaatttgagtgacatgaagaaggctaatttatgtagctggattattgatgcagATAGTTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACCCTTGTTGTTCCAGAGTTGGATCATACTTCTTTCTGGAAAGACACCAG
- -ggcgggg
- - - - - - - cagacac
- - - - - - - - - - - - - - - - - - - - - gatacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtagctg