Sequence
atgc intronic sequence ATGC exonic sequencegtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgttttgtgttatttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
Basic information
species | Glycine max |
transcript | GLYMA13G16170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gtatggcaagagttttggaatatttgttcatgat-tattcttgatgggtgaccatatcaaatggttgttttg-tgttatttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
| | | |||| || || | ||| ||| | | | || ||| | | | | ||||||||||| ||| || || || || ||| | |||||||||| || ||||||||||| || || ||||| ||||| ||||||||||| || || || || |
--------------gttggacatttatttttgttatatgtaagataataaatagtgtttcatcaatgtacaactactctctcgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 6
gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgttttgtgttatttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
| || || || || | | | || |||| || | | || || | || ||| | |||||||||||||| || ||||| || || ||||||| ||||| ||||| || |||||||| || ||||| || || ||||| ||||| | ||||| || |
-----------------gtgaatatgacaataatgaattatcattac--acca-atttactttttattaacttttctttctacacagGGAACTGTTGTGGAAGGAACAATTGAACAATTATTCGAAGGCCACCACATTAATTACATTGAGTGCATTAACGTGGACTATAAATCTAACAGAAAAGAAT
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 6
gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgttttgtgttatttgtct-tcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
| ||||| | || ||| ||| | || ||| | || | ||| || | |||||||||||||| ||||| || ||||| | ||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||| || || |||||||
---------------------gtacaaacatgactgttgttg-tgg--aattatttcagtt--ctgacaattattaagtgcttgccagGGAACTGTTGTGGAGGGCACTATACAGCAGTTATTTGAAGGGCACCATATGAACTACATTGAATGCATCAATGTGGACTACAAATCTACAAGGAAGGAGT
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgtt-ttgtgttatttgtctt---cagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
| | | ||| | | || ||||| | ||||| | | | | | | | || | | | | ||| |||| || | || ||||| || |||||||| | |||||||| || ||||||||||| || |||||||||||||| || | || || ||| | |||||||
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatggcaagagttttggaa--tatttgttcatgattattc----ttgatgggtg-accatatcaaatggttgtt-ttgtgttatttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
|||||| | | | || | ||| | ||| | || | | | ||||| | || | | |||| | | | | | | | |||||||||| ||| ||||| || || || || | || |||||||| || ||||| |||||||| ||||||||||| || || |||||||| | || ||||
gtatggataaatctctgttagctatgtcttctcggttttcaagagtagctgggtacattatgtttactggtgggaatccttctgtgcttttacagGGAACTGCTGTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGT
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgttttgtgtta--tttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
||| | |||| | || | ||||| || | | | | || ||| | |||| |||||| || |||||||| | | || ||||| || ||||||||||| || |||||||||||||| ||||| || || ||| ||||||| |
-------------------------gtttactgctattttct--------tcacgttaaatg-ttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
upper sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgttttgtgtta--tttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
||| | |||| | || | ||||| || | | | | || ||| | |||| |||||| || |||||||| | | || ||||| |||||||||||||| || |||||||||||||| |||||||| || ||| ||||||| |
-------------------------gtttactgctattttct--------tcacgttaaatg-ttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattcttgatgggtgaccatatcaaatggttgttttgtgttatttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
tcttgat putative branch site (score: 4)
tttgtcttc putative PPT
atatcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgttttgtgttatttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG