Sequence
atgc intronic sequence ATGC exonic sequence...agattttttttgtggccactgtttttgcaactgtattacatgcatgatagtcatatttgacgttccatggctgactggctgtattcttttcattatgtagATAACCACCAGGGTAACAGCAGCCCATTATGGTGTTAAGCTCAGCCCTTCTTTCCTGGTGCCATCAAATTGGACAGGTTGCTTAGGAGTGATGAATAATT
Basic information
species | Glycine max |
transcript | GLYMA01G45240.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G45240.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G17870.1 (Arabidopsis thaliana), 3'ss of exon 3
agattttttttgtggccactgtttttgcaactgtattacatgcatgatagtcatatttgacgt-tccatggctgactggctgtattcttttcattatgtagATAACCACCAGGGTAACAGCAGCCCATTATGGTGTTAAGCTCAGCCCTTCTTTCCTGGTGCCATCAAATTGGACAGGTTGCTTAGGAGTGATGAATAATT
| | | |||| | | | | || |||| || | |||| | ||| | || || | | ||||| | || || ||||| || || | | ||||| || | ||||| || || || ||||||||||||||||| |||||||||||||| ||||| ||||
--------------gtaa--gccgaagcaaattaaaagaactaactccaggttcctttgctgtatacatg--taactaaacctgttagttctttgcttcagATAGCAACTAGAGTAACCGCTGCGCGACACGGTGTCAAATTAAGCCCGTCGTTTCTTGTGCCATCAAATTGGACTGGTTGCTTAGGAGTTATGAACAATT
upper sequence: GLYMA01G45240.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0088g00320.t01 (Vitis vinifera), 3'ss of exon 3
----agatttttt-ttgtggccactgtttttgcaactgtattacatgcatgatagtcatatttgacgttccatggctgactggctgtattcttttcattatgtagATAACCACCAGGGTAACAGCAGCCCATTATGGTGTTAAGCTCAGCCCTTCTTTCCTGGTGCCATCAAATTGGACAGGTTGCTTAGGAGTGATGAATAATT
|| | | | || | || | | | |||| | | | | || | || |||| | || || || || || |||||||| |||| |||||||||||||| | |||||||||||| |||||||| || || || |||||||| || |||||||| ||| | ||||| ||||| || |
tgtaaggtcctacatcttgaatatgattctaatgattttatttttcctgtcagaacc-tacaacccctttcatgtgt---tgaaagt-ttgcttgtatcttgtagATAGCCACAAGGGTAACAGCAGCTCGTTATGGTGTTAAACTCAGCCCATCATTTCTTGTGCCATCTAACTGGACAGGGTGCCTGGGAGTTATGAACAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatagtcatatttgacgttccatggctgactggctgtattcttttcattatgtagATAACCACCAGGGTAACAGCAGCCCATTATGGTGTTAAGCTCAGCCCTTCTTTCCTGGTGCCATCAAATTGGACAGGTTGCTTAGGAGTGATGAATAATT
ggctgac putative branch site (score: 3)
ttcttttcatt putative PPT
tattcttttcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agattttttttgtggccactgtttttgcaactgtattacatgcatgatagtcatatttgacgttccatggctgactggctgtattcttttcattatgtagATAACCACCAGGGTAACAGCAGCCCATTATGGTGTTAAGCTCAGCCCTTCTTTCCTGGTGCCATCAAATTGGACAGGTTGCTTAGGAGTGATGAATAATT
- - - -ttttgtg
- - - - - - - gccactg
- - - - - - - - - - - - - gcaactg
- - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggctg