Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataacattgtgttattgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
Basic information
species | Glycine max |
transcript | GLYMA13G41520.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 6
--tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataa-cattgtgttattgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
| |||| | ||| | | ||| |||| | | ||| |||| | ||| | |||| | || || | | | ||||||| ||||||||||| || |||||| | |||||||||| ||||| |||| || |||||||| || ||||| ||||||||||||||||| || |
attttgtg-gggtgtcttgctacca-gttacttttgtccatgtttgt-tttctggcactgaatgtgcaacagtgttgtttgaccaaatgttatttgtcttaagGCTCCCCAGAAGCACCAAAAGTATGTTGCTAATGTTCTTGGTCTTCCACAATCAAGAGTTGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
upper sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 2
-tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataacattgtgttattgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
| | | | || | || || | || | ||| || | | | || | | ||| | ||| || | | || ||||||| |||||||| ||||| |||||| | ||||||||| ||||| ||||| || |||||||| || ||||| ||||||||||||||||| || |
ttctttttatgttgcttctggttgtttccatattat-ttgcattatactacctgtttagtctctgtcattgccaatttgtcatattgttctttatttttagGCTCCGCAGAAGCATCAGAAGTATGTTGCAAGTGTTCTTGGTCTTCCACAATCAAAAGTCGTTTGCAAGACTAAGCGTATTGGTGGTGGATTTGGTGGAA
upper sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------------tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgca-ttgtgaaaataaca----ttgtg--ttat-tgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
| || || || | | || ||| | | | ||| | || ||| | || || | |||| ||||| |||| ||||||||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| || || || |||||||| || |||||||||||||| ||||| || |
gtaagcatattattagtgtactgccatatactttactgagtggaattcatttttattcttggtttgtcggaccagtacatgaccattaagtctctgtacaagaaaactattaggcatcagctagtttaagat-attatatgataatgttgtctctgcttaagcaaatgttggtggttgtgatttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
upper sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------tgtgtgtgagtgagtg-agtgtagtgtttggcttgtattggcctaaatttatggcttg-aaggaaataactgcat-tgtgaaaat----aacattgtgttat-tgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
| | | || | | || ||| | | ||| | | | || | | |||| | || || || | || |||| | ||||||||||| |||||||||||||||| || ||||||||||| ||||| ||||| || || || |||||||| || ||| |||||||||| ||||| || |
gtgagcatattatttagtatttacatcatttagaataacgtacaaaaaaccattaggcatcagccagtttaagatattaaatgataatgttgtctctgcgtatgccaatattggtagttatgatttatatacagGCTCCTCAACAGCACCAGAAATATGTGTCTCATGTTCTTGGTCTTCCAATGTCTAAAGTGGTATGCAAAACCAAACGACTTGGTGGTGGCTTTGGTGGTA
upper sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 6
tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataact--gcattgtgaaaataacattgtgttattgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
| | || | | | ||| | | || || | | ||| | | | | | ||| ||| | | | | ||||| ||| |||||||| |||||||||||||| ||||||||||| ||||| |||||||| |||||||||||||| |||||||| |||||||||||||||||||
tatttgcctagaaatttat-tagcaatggatgccagttcaactgc-tctgtggtggtcacagccttatttagaattttgacagatttgatctttatgtgcagTGTCCCCAGAAGCATCAGAAATATGTTTCTCATGTTCTTGGTCTTCCAATGTCAAAAGTAGTTTGCAAAACCAAGCGAATCGGTGGTGGATTTGGGGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatggcttgaaggaaataactgcattgtgaaaataacattgtgttattgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgcattgtgaaaataacattgtgttattgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
-gtgtgtg
- - - - - - - tgagtgt
- - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - -tggcttg
- - - - - - - - - - - - - - -gcttgta
- - - - - - - - - - - - - - - - - - - -gcctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa