Sequence
atgc intronic sequence ATGC exonic sequence...ctttccttgtatttctttgtagtaggatttctgtggtattatatataggttctgcatctatgaacttgactagatccttttgtgttgcatgctaatgtagTGGGATTGGCATTGTTAATGCTATTGAGGTTGTGAATGCATTCCCTGAGGAAGATGGCCTCCTGAAATTCCGGCAATGGGTTGAGTCACCGGATCCCACC
Basic information
species | Glycine max |
transcript | GLYMA01G16370.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g10780.1 (Oryza sativa), 3'ss of exon 9
-ctttccttgtatt-tctttgtagtaggatttctgtggtattatatataggttctgcatctatgaacttgactagatccttttgtgttgcatgctaatgtagTGGGATTGGCATTGTTAATGCTATTGAGGTTGTGAATGCATTCCCTGAGGAAGATGGCCTCCTGAAATTCCGGCAATGGGTTGAGTCACCGGATCCCACC
|||| || | ||| | ||| || | || ||| | ||| | | | | || ||| | | || | ||| ||||| ||||||||||| ||||||||||| |||| | ||||| |||||||||||||| |||| || ||| || | |||||||| ||||| ||||| ||
actttaattatgccatctcaatttcttattttgaaggggggaaaatgccatttcagtttctgttttgtccagtgtatttatttatatac--tgattatgcagTGGCATTGGCATTGTGAATGCTATTGAAGTTGCACACGCATTTCCTGAGGAAGATGGGCTCCAAAAGTTCAGGGAGTGGGTTGAATCACCAGATCCAACT
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G28030.1 (Arabidopsis thaliana), 3'ss of exon 12
ctttccttgtatttctttgtagtaggatttctgtggtattatatataggttctgca-tctatgaacttgactagatccttttgtgttgcatgctaatgtagTGGGATTGGCATTGTTAATGCTATTGAGGTTGTGAATGCATTCCCTGAGGAAGATGGCCTCCTGAAATTCCGGCAATGGGTTGAGTCACCGGATCCCACC
| | | ||| | || | | | |||| || | |||| | |||| || || || ||| ||| ||||| ||||| ||||| ||||||||||| ||||||| ||| || || ||||| ||||| || | |||||| || |||||||||| ||||| ||||| |||
----------------gttagctgaggttttaactgcataaggtcaaagttccgctctttatgtaattgatatcataatt--gttttga-----catgcagTGGTATTGGTATTGTCAATGCTATTGAAGTTGTGACTGCTTTTCCCGAGGAGGATGGGCTTCAGAAATTTCGTGAATGGGTTGAATCACCTGATCCAACC
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv14s0066g01630.t01 (Vitis vinifera), 3'ss of exon 10
ctttccttgtatttctttgtagtaggatttctgtggtattatatataggttctgcatctatgaacttgactag-atccttttgtgttgcat--gctaatgtagTGGGATTGGCATTGTTAATGCTATTGAGGTTGTGAATGCATTCCCTGAGGAAGATGGCCTCCTGAAATTCCGGCAATGGGTTGAGTCACCGGATCCCACC
||| ||| | || | | | | | | || | | ||| | || | | | | || || | | ||| | | ||||||||| ||||||||||||||||||||||| ||| | ||| | || |||||||| || || || | || |||||| | |||||||| ||||| ||||| | |
-tttatcagtagatac--acaggatgtatacacagatgttgagttcatgtttattaagtaaatatctaatttttatttttattttttggttcaaatgatgtagTGGAATTGGCATTGTTAATGCTATTGAAGTTTTAAATTCTTTTCCTGAGGAGGACGGTCTTCATAAGTTCCGGGAGTGGGTTGAATCACCAGATCCAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggttctgcatctatgaacttgactagatccttttgtgttgcatgctaatgtagTGGGATTGGCATTGTTAATGCTATTGAGGTTGTGAATGCATTCCCTGAGGAAGATGGCCTCCTGAAATTCCGGCAATGGGTTGAGTCACCGGATCCCACC
tgctaat putative branch site (score: 2)
taatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttccttgtatttctttgtagtaggatttctgtggtattatatataggttctgcatctatgaacttgactagatccttttgtgttgcatgctaatgtagTGGGATTGGCATTGTTAATGCTATTGAGGTTGTGAATGCATTCCCTGAGGAAGATGGCCTCCTGAAATTCCGGCAATGGGTTGAGTCACCGGATCCCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - ccttgta
- - - - - - - - - - - - - - -tctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaac