Sequence
atgc intronic sequence ATGC exonic sequence...gaacccgtgtgtgtgagtgttagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataacattgtgttgttgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
Basic information
species | Glycine max |
transcript | GLYMA15G03870.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 6
gaacccgtgtgtgtgagtgttagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataa-cattgtgttgttgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
| ||| | || || || || | ||| |||| | ||| | |||| | || || | | | ||||||| ||||||||||| || |||||| || |||||||||| ||||| |||| || |||||||| || || || |||||||||||||||| || |
-attttgtggggtgtcttgctaccagttacttttgtccatgtttgttttctggcactgaatgtgcaacagtgttgtttgaccaaatgttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
upper sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------------------------------------------------------gaacccgtgtgtgtgagtgttagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgca-ttgtgaaaataaca----ttgtgttgt---tgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
| | ||| || || || ||| | | | ||| | || ||| | || || | |||| ||||| | | ||||||||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| || || || |||||||| |||||| |||||||||| ||||| || |
gtaagcatattattagtgtactgccatatactttactgagtggaattcatttttattcttggtttgtcggaccagtacatgaccattaagtctctgtacaagaaaacta---ttaggcatcagctagtttaagat-attatatgataatgttgtctctgcttaagcaaatgttggtggttgtgatttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
upper sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------gaacccgtgtg-tgtgagtgttagtgtttggcttgtattggcctaaatttatggcttg-aaggaaataactgcat-tgtgaaaataac--attgtgttgt---tgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
| | | || | || ||| | | ||| | | | || | | |||| | || || || || || | | | ||||||||||| |||||||||||||||| |||||||||||||| ||||| ||||| || || || |||||||| |||||| |||||||||| ||||| || |
gtgagcatattatttagtatttacatcatttagaataacgtacaaaaaaccattaggcatcagccagtttaagatattaaatgataatgttgtctctgcgtatgccaatattggtagttatgatttatatacagGCTCCTCAACAGCACCAGAAATATGTGTCTCATGTTCTTGGTCTTCCAATGTCTAAAGTGGTATGCAAAACCAAACGACTTGGTGGTGGCTTTGGTGGTA
upper sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 6
gaacccgtgtgtgtgagtgttagtgtttggcttgtattggcctaaatttatggcttgaaggaaataact--gcattgtgaaaataacattgtgttgttgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
| | | | |||| | | || || | | ||| | | | | | ||| ||| | | | | ||||| ||| |||||||| |||||||||||||||||||||||||| ||||| |||||||| |||||||||||||| || ||| | |||||||||||||||||||
-tatttgcctagaaatttattagcaatggatgccagttcaactgc-tctgtggtggtcacagccttatttagaattttgacagatttgatctttatgtgcagTGTCCCCAGAAGCATCAGAAATATGTTTCTCATGTTCTTGGTCTTCCAATGTCAAAAGTAGTTTGCAAAACCAAGCGAATCGGTGGTGGATTTGGGGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatggcttgaaggaaataactgcattgtgaaaataacattgtgttgttgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
aaataac putative branch site (score: 2)
aaaataacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaacccgtgtgtgtgagtgttagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataacattgtgttgttgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - gtgtgtg
- - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - -tggcttg
- - - - - - - - - - - - - - -gcttgta
- - - - - - - - - - - - - - - - - - - -gcctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa