Sequence
atgc intronic sequence ATGC exonic sequencegtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcttggccctttcataacatcaatttttttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
Basic information
species | Glycine max |
transcript | GLYMA13G25110.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
---------gtaatatcagtgtctttgtggcatgtatgtt-gtattcttctggtcttggccctttcataacatcaatttttttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
|| | || | || ||| | || | | || | ||| | | | ||||||| || |||| ||||||||||||||||| || ||||||||||| |||||||| || || | |||||||| ||||| ||||| ||||| || || |||| || || | ||||
gtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaatttt---ggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
upper sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 5
----------gtaatatcagt---gtctttgtggcatgtatgttgtattcttctggtcttggccctttcataacatcaatttttttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
||| | | | | || | || || || || | | || | || || || || | || ||| | |||||||| |||||||||||||| || |||||||||||||| | ||||| || || |||||||| || ||||||||||| || || | ||||
gtttgttcatttaacctgaattcagctcttctcctattgataatgcctttgttta--ctggctaacttaattcaatttataatgttt--cagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTTAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGAGAGTGGG
upper sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 8
----gtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcttggccctttcataac----atcaattttt--ttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
|| | | | | | | | |||| | | |||| | | || | | ||||| |||||| | | |||| | |||||||| |||||||||||||| || |||||||||||||| | ||||| || || |||||||| || ||||||||||| || || | ||||
gtttgttcttttaatctgaatttcagatgt-tctcctattgataatgcctctgttactggataacttggatcaatgtacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG
upper sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcttggccctttcat--aacatcaatttttt--tcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
| ||| | ||||| | | | | || ||| ||||| | | | | | | | ||| | || | |||||||||||||| ||||| ||||| || |||||||| || || || ||||||||||| ||||| ||||||||| ||||||| ||| | || |||||||
-----gtgagt-ttattgtgacttatctttttaattattctgattggaatcgagttgttcacctttaatctcttctttgacagAGATATGGTCCGCCTCCTTCTTACCCACATCTGAAAATTCCTGGTTTGAATGCTCCTATTCCAATTGGAGCTAGCTTTGGTTTTCATGCTGGCGGCTGGG
upper sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtaatatcagtgtctttgtggcatgt-atgttgtattct--------tctggtcttggccctttcataacatcaattttt-ttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
|| | || || ||| | ||| | || ||| | | | ||| || | | | | | | ||| || |||||||||||||| || ||||| ||||| |||||||| ||||| || |||||||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||
gtcagatgagctaatttctcgcaattgattttgacctttacagaaccttcaactttgttttttcctttagctgactgtttatttttcagAGATATGGTCCGCCACCATCATATCCACATCTGAAAATCCCTGGGCTGAATGCTCCTATTCCTCCTGGTGCTAGCTTTGGTTATCATCCTGGTGGTTGGG
upper sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S98_7V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------------------------gtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcttggccctttcataacatcaatt----tttttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
||| | || | | | || || | |||| | || || || | || | | |||||| ||||||||||| |||||||| |||||||||||||| ||||| || || |||||||| || || || || || |||||| || ||| | || |||||||
gtgcgtgcagttgctctccactcttgtgaagttagggagtaaatctttttctttttactcaacattacacgtgtaacctgaactttttactgttatgaatgaagactattctgcaaattttgtttttcatgcctctgttagtg-cctttggctgactttgtctgcggtttttctgcagAGATATGGGCCTCCTCCTTCTTATCCTCATCTTAAGATTCCTGGATTGAATGCACCAATACCAGAGGGGGCCTCTTTTGGCTATCATGCTGGAGGCTGGG
upper sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------gtaatatcagtgtctttgtggcatgtatgtt-gtatt-cttctggtct-tggccctttcataacatcaatttttttcac--cagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
| ||| | | | | | | | | ||| ||| | | |||| | ||| | || | | ||| || ||||||||||| ||||||||||||||||| || || ||||| || || |||||||| || || || || ||| |||||| || ||| | || |||||||
gtgcgtggctttgcttaaatttcttgtgctttaaggaagcatgtctgtttcttttgagtcgtcattatatctctaaccttgacgtttgtaatacgtctgaaatgcaaatcttagtttttattcctctgttttactgcagAGATATGGGCCTCCTCCATCTTATCCCCACCTTAAGATTCCTGGATTGAATGCACCAATACCAGAGGGTGCTTCTTTTGGCTATCATGCAGGAGGCTGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatgttgtattcttctggtcttggccctttcataacatcaatttttttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
tcataac putative branch site (score: 2)
tttttttcacc putative PPT
tttcataacatcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcttggccctttcataacatcaatttttttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT