Sequence
atgc intronic sequence ATGC exonic sequencegtacactatctttgtagtttaaagatgatctgctttcatagactcttaaatgatttcttacttctgcttgattgactgattgattttgaaatgatagtttgatacaaaaatgaatatactattgccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
Basic information
species | Glycine max |
transcript | GLYMA09G42180.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacactatctttgtagtttaaagatgatctgctttcatagactc-ttaaatgatttcttacttctgcttgattgactgattgattttgaaatgatagtttgatacaaaaatgaatatactattgccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
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----------------------------------gtaactccctcattaagtcaaaccttttctctttttctttctctg--caacttcgagacatttatttcgacc---------ttttacgttgccg--tttcagGAAGCTTTAGATATTGTGCATGTTAGTAAAGAAGATCAAGAAAATGTATTTGCAATGCTTGCTGCAGTATTATGGCTAGGGAATGTTTCTTTTACCATTA
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
gtacactatctttgtagtttaaagatgatctgctttcatagactcttaaatgatttcttacttctgcttgattgactgattgattttgaaatgatagtttgatacaaaaatgaatatactattgccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
| || || | || ||| || |||||| || || | | ||| ||| | | || || | | || | | | || || ||||||||||| || |||| || | || |||||||| || || | |||||||||||||||||||||||| |||||| | |||||| | || || || || |
------------------------gtaattctctctttcag----ttagatactttcttcctcctcttc--tctactcatt--tcagacctttatttttctgtttattgatttaaaagtttctgttg--ttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
gtacactatctttgtagtttaaagatgatctgctttcatagactcttaaatgatttcttacttctgcttgattgactgattgattttgaaatgatagtttgatacaaaaatgaatatactattg-ccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
||| ||| | || ||||| ||| | ||| |||| || || || || || |||| | || | |||| ||| | | | || || ||||||||| | ||| |||| || |||| ||||| ||||| |||| ||||||||| |||||||||||||| || ||| | ||||| | || ||||||||||
-----gtattttt-tcccttcttgatgactaaacccaata------ttaatcattt-ttgtacctattttcttctcta--tgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattttgaaatgatagtttgatacaaaaatgaatatactattgccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
gtttgat putative branch site (score: 5)
cttcc putative PPT
atacaaaaatgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacactatctttgtagtttaaagatgatctgctttcatagactcttaaatgatttcttacttctgcttgattgactgattgattttgaaatgatagtttgatacaaaaatgaatatactattgccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG