Sequence
atgc intronic sequence ATGC exonic sequence...taaatcttaagatgtataccatgttttttggatgcgttaaacttgtagtgtttgaggtggcattgtttttgctgttaatgatttatttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
Basic information
species | Glycine max |
transcript | GLYMA20G33270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
taaatcttaagatgtat-accatgttttttggatgc-gttaaacttgtagtgtttgaggtggcattgtttttgctgttaatgatttat-ttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
|| || || | | | || ||| | || | | || ||| || || | | | | | | | | | ||||||| ||||| |||||||| || || ||| | ||||||||||||||||| || || || ||||||||||| || || || ||||||||||| || || ||
--tattctactgcacattggtagactggccaaacgctattatatgcataccactattga-ggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 2
----taaatcttaagatgtataccatgttttttggatgcgttaaacttgtagtgtttgaggtggcattgtttttgctgttaatgatttatttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
| || | | | | | | |||| |||| || ||||||| || || | | | | | | | | | ||||||| ||||| |||||||| || || ||| | || |||||||||||||| ||||| || ||||||||||| || || || ||||||||||| || || ||
attgctagactggccaaacacaaaactatatgcatatgcagcaaaccgcta----ttgaggtatttgaattaatgtaatctaaatgtgctatttttttggacagACACGAAGGCTTGGGAAGTTGATACTTTGCGGGGACACATGAATAATGTGTCATGCGTGATGTTCCATGCTAAGCAAGACATCATTGTGTCCAACTCAGA
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 2
-taaatcttaagatgtataccatgttttttggatgcgttaaacttgtagtgtttgaggtggcatt-gtttttgctgttaatgatttatttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
||| || | || | | || | | | ||| | | ||| | | | | | | | ||| | | || | | | | ||| ||||||| ||||| |||||||| || || ||| | |||||||||||||| || || ||||| ||||||||||| || || || ||||| ||||| || || ||
gcaaactttgtggggtgtggaacattcacttccactatcaccattgcattatttaaagggataataggtgatgcaatcta-aatgtgctgtttt-ttgacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAACGTGTCCTGTGTGATGTTCCATGCAAAGCAAGACATCATAGTGTCCAACTCAGA
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010054_T01 (Zea mays), 3'ss of exon 2
taaatcttaagatgtataccatgttttttggatgcgttaaactt-gta-gtgtttgaggtggcattgtttttgctgttaatgatttat-----ttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
||| | | | | || || | || || ||| ||| || | || | ||||| || ||| || ||| |||| ||| | |||| || ||||| |||||||| || || || || || |||||||||||||| || ||||| ||||||||||| || || || ||||| |||||||| || ||
-----tttagcagatcaatta-gtacttagcatatgtgaaaaagagtatacattctacaaggaaatgtttgaaatgc-aataatctatatgtgttctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGCCACATGAATAATGTGTCTTGTGTGATGTTCCATGCGAAGCAAGACATCATCGTGTCAAACTCAGA
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 2
taaatcttaagatgtataccatgttttttggatgcgttaaact-tgta-gtgtttgaggtggcattgtttttgctgttaatgatttat-----ttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
|| || ||| | || | | || || ||| | || || | || | | ||| || ||| |||||| ||| ||| | |||| || ||||| |||||||| || || || || || ||| |||||||||| || ||||| ||||||||||| || || || ||||||||||| || || ||
------tttagctgttcaattagtacctagcatatgtgaaagaatatatacattctacaaggaaatatttggaatgc-aataatttatgtctgctctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGTCACGTGAATAATGTGTCCTGTGTGATGTTCCATGCGAAGCAAGACATCATTGTGTCTAACTCAGA
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------taaatcttaagatgtataccatgtt-ttttggatgcgttaaacttgtagtg---tttgaggtggcattgtttttgctgttaatg-atttatttctctattgt--cagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
| ||| | | ||| | | || || |||| |||| | | || | || | ||| | | || ||| ||| | | ||| | |||| || || || ||||| ||||| || ||| |||| || |||||||| ||||||| ||||||||||||||| |||||||| || ||||| ||||| |||||
gtaattatttggtggtatacttttgtgcttacaatttttatatgctatcaatcgtcaatgatgttactgatatgaaaatattctgcatgccttaatccttagatgaatctcgaaattgcaaagacga-gttggtaacatgtttttaacgatatcattgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGCCATATGAATAACGTTTCATCTGTTATGTTCCATGCAAAACAGGACATAATTGTATCAAACTCTGA
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
-taaatctta-agatgtataccatgttttttggatgcgttaaacttgtagtgtttgaggtggcattgtttttgctgttaatgatttatttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
|| ||||| ||| | | | | || || | ||| || ||| | | ||||| | | | ||| || | | ||| |||| || || || ||||| ||||| || ||| |||| || |||||||| ||||||| |||||||||||||| |||||||| || || |||||||| |||||
gtatttcttatggatatctgtcttcttcttcaca-----gaaagtta----attttatgaatcattga----ggtactgatgcgtttcaattttgttg-cagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 3
-taaatcttaagatgtataccatgttttttggatgcgttaaacttgtagtgtttgaggtggcattgtttttgct----gttaatgatttat-ttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
| ||| | ||| | | | |||| | | |||| || ||| || || | |||| | ||| ||| | ||| || |||| | |||||||||||||| |||||||| || || ||||| |||||||||||||||||||||||||| | || ||||| | |||||| | |||||||||||||| ||
tttcatcc--atttgttaatcgtattttct--ttttgttagggttatagaacttt--gtagaattgaactagctaatggtttgcaacttaccttttctactttcagACACAAAGGCTTGGGAAGTAGATACTTTGAGGGGGCACATGAATAATGTTTCATGTGTCTTCTTTCATGCAAGGCAGGATGTGATTGTGTCAAATTCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtgtttgaggtggcattgtttttgctgttaatgatttatttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
tgttaat putative branch site (score: 3)
tttatttctctatt putative PPT
ttaatgatttatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaatcttaagatgtataccatgttttttggatgcgttaaacttgtagtgtttgaggtggcattgtttttgctgttaatgatttatttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
- - - - - - - - - ccatgtt
- - - - - - - - - - - - - - tggatgc
- - - - - - - - - - - - - - - - - - - - - -tgtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt