Sequence
atgc intronic sequence ATGC exonic sequence...atttcattgtatcatagtttagaaggcttggtggtggttgtggttgtggttgtcataatgcaatgtctcagttcataacatatatgctattgcggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATAAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
Basic information
species | Glycine max |
transcript | GLYMA12G30520.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------------------atttcatt-gtatc----atagttta-gaaggcttggtggtggttgtggttgtggttgtcataatgcaatgtctcagt-tcataacatatatgctattgcggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATAAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
|||| || || ||||| || || |||| | || | || | || || | | | | || || | || | ||||| || ||| | || ||| || | || || |||||||| |||||||| ||||| || || || |||||||||||||| ||||| ||||| || |||||
gtaagttgtactttgcaacagtaatactgtttgattctatatatgtttttttggtactttggtaatgtttcgttcacattcctgatagtctataaatgcttcattcgcattaaatccccgtgagtgaaaactt--tgccataatgtgatggtatttcatctgtctt--cacagGAAAACATGTCTAGGATGCTGTTAGTAACAGATGTACAGGATATCATTAAAAGGCACCAGGCCCAGATTATTACCTCTTTGAAAGATCCAGATATCAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
---atttcattgtatcatagtttagaaggcttggtggtggttgtggttgtggttgtcataatgcaatgtctcagttcataacatatatgctattgcggt-gcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATAAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
| || ||| || | || || | | | || || || || | | || || |||| | || | | | ||||| |||||||| | ||| ||||||| || ||||| |||||||||||||| | ||||| ||||||| || ||||| ||||| || |||||||||||
gtgagatc-ttgcataccacttcctgcatctaagcc-tagctggagtagtttgtgaagtggttggtggtttc---tcatgatgcattttttgacaaaattacagGAAAATATGACGCGGATGCTGATGGTCACAGATGTTCAAGATATCATAAAGAAGCATCAGTCTCAGATAATCACCTCCTTGAAAGACCCTGACATCAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 9
------------------atttcattgtatcatagtttagaaggcttggtggtggttgtggttgtggttgtcataatgcaatgtctcagttcataacatatatgct-attgcggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATAAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
| ||| || ||| || |||| | || | | ||| | | | || |||| | | | ||| | || || | | | ||||||| |||||||| ||||| ||||||| || ||||| |||||||||||||| | ||||| ||||||| || ||||| ||||| || |||||||||||
gtgagatcttgcatacccacttc-ctgcatctaagcttagctagaacagtaat-----ttgttaagtatttggtagtgcattatgtggcttctcatgatgcttgttgacaacattgcagGAAAATATGACGCGAATGCTGATGGTCACAGATGTTCAAGATATCATAAAGAAGCATCAGTCTCAGATAATCACCTCGTTGAAAGACCCTGACATCAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------------------------atttcattgtatcatagtt-tagaaggcttggtggtggttgtggttgtggttgtcataatgcaatgtctcagttcataa-----catatatgctattgcggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATAAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
||| | ||||| | | | | || | | ||| | | |||||| ||||| | | ||| | ||| || || | | ||||||| || ||||| | ||| ||||||| | ||||| || ||||| || ||||||||||| ||||| || || |||||| |||||||||||||||||||
gtaagttacaggatggttctatctgtgcttccgttatgtcttcacctatatccaatgattaaagcatatcaaactggcatgcaccatgttagaatttgaatggattgatgtcattgcttgctgtctaactgcatgatttgacatttagattactctgctgcagGAAAACATGACTCGGATGCTGATGGTGTCCGATGTGCAGGATATTATTAAAAGACATCAGGCTCAAATCATAACCTCACTGAAGGATCCTGACATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggttgtcataatgcaatgtctcagttcataacatatatgctattgcggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATAAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
tcataac putative branch site (score: 2)
ttcataacatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttcattgtatcatagtttagaaggcttggtggtggttgtggttgtggttgtcataatgcaatgtctcagttcataacatatatgctattgcggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATAAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatatgc