Sequence
atgc intronic sequence ATGC exonic sequence...tttgacttgaaacagttagtttacattagttatcatttatatgaggtggaaatagaatattccatgaataatcatctaactcagttccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
Basic information
species | Glycine max |
transcript | GLYMA09G33240.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 7
tttgacttgaaacagttagtttacattagttatcatttatatgaggtggaaatagaatattcca---tgaataatcatctaactcagt--tccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
| | | || | || || | | || | || |||| |||| | | | | | | | ||| | ||||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||| || ||||| | ||
------------------------gtaaaacgttatct-tagtagacaaatgtcctattcttcaccctgaaaaatccagtcattgattcgtatatatgtgtatagCAACCGAAGAGGAAGCAGCAGAGGCTTATGACATTGCAGCCATAAAGTTCAGAGGAATCAACGCAGTAACTAACTTTGAGATGAACAGGTATGACATTGA
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G10510.3 (Arabidopsis thaliana), 3'ss of exon 7
tttgacttgaaacagttagtttacattagttatcatttatatgaggtggaaatagaatattccatgaataatcatctaactcagttccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
| || | | | | | | || | | | ||| || || || |||| | || | | | | || |||||| || ||||||||||| || || ||||| || ||||| || || |||||||| |||||| ||||| |||||||||||||| | || || || ||
-----------gtatgtaaaat-cttcaaacttggtctagctaatttaacaatc--attgtctgtggttaattagttagtcctggtgt-tgttgttgtagCAACGGAAGAGGAAGCAGCTGAAGCGTATGACATAGCAGCAATCAAATTCAGAGGAATAAACGCTGTAACTAACTTTGAGATGAACCGTTACGACGTTGA
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 7
tttgacttgaaacagttagtttacattagttatcatttatatgaggt----ggaaatagaatattccatgaataatcatctaactcagttccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
| ||| || | | ||| || | || | | | ||| || || ||||| ||||| ||| | || | | |||| |||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| |||| || || || ||||| || |||||||| |||||||||||||
ggtcactggacgtgctaaaattaggctaat-gtcttaaaagaggggtctcaaaaagaagcatattgttcacataataatc---ccttgtaactcgtggtgtcagCCACCGAAGAGGAAGCAGCAGAGGCATATGACATAGCAGCCATAAAGTTCAGGGGTGTGAATGCGGTGACCAATTTCGAGATGAACCGATATGATGTGGA
upper sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0772g00020.t01 (Vitis vinifera), 3'ss of exon 6
tttgacttgaaacagttagtttacattagttatcatttatatgaggt----ggaaatagaatattccatgaataatcatctaactcagttccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
| ||| || | ||| || | || | | | ||| || || ||||| ||||| ||| | || | | ||||| |||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| |||| || || || ||||| || |||||||| |||||||||||||
ggtcactggacgtgctataattaggctaat-gtcttaaaagaggggtctcaaaaagaagcatattgttcacataataatc---ccttgtaactcgtggtatcagCCACCGAAGAGGAAGCAGCAGAGGCATATGACATAGCAGCCATAAAGTTCAGGGGTGTGAATGCGGTGACCAATTTCGAGATGAACCGATATGATGTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggaaatagaatattccatgaataatcatctaactcagttccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
atctaac putative branch site (score: 2)
aatagaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgacttgaaacagttagtttacattagttatcatttatatgaggtggaaatagaatattccatgaataatcatctaactcagttccacatggtaacagCAACCGAGGAGGAAGCAGCAGAGGCATATGATATTGCAGCCATTAAGTTCAGAGGTGCAAACGCAGTAACCAACTTTGAGATGAATAGATATGATGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- tgacttg
- - - - - - - - - - - - - - - - - - - - - gaggtgg
- - - - - - - - - - - - - - - - - - - - - - - - -aaatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttccac