Sequence
atgc intronic sequence ATGC exonic sequence...acatctgctaatttggtagtttgggattcttgttttacttgaagcacaagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
Basic information
species | Glycine max |
transcript | GLYMA13G23230.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 2
acatctgctaatttggtagtttgggattcttgttttac--ttgaagcacaagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
| | | || |||| || | | | | | | ||| || || | || | | || ||| | ||||||| || |||||||| ||||| |||||||| ||| | | ||||| || |||||| |||||||||||||||| |||||||| |||||||||||||||||||
-ccggtttgatcttaaaagttgggcagaaaaagtcaagagtcagtcagttaccttgtatttg-aagtatttctgacggaatccatctgttgttataccacagACTACACATGTTGCAGCACAGTATGGTCAAACATCATATCTTTATCATATTGTTGCAAAATGGAATGCTGATCCTGATGTCCCTGATAATGATGGAAGAA
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 2
acatctgctaatttggtagtttgggattcttgttttacttgaagcacaagcgtgtggctgtaaatgttaatt--ttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
|| | | | | | || || | ||| || | | | || || | || |||| ||| || | | |||| | ||| |||| |||||||| || || ||||| |||||||| || |||| || |||||| | || ||||||||||| || ||||| |||||||||||||||||||
-aatttaacctatgaattctctaggtaaaatgaaaagcaagaatcaacaacttttgtctatggcagtgaatttgttaaaaactctatactgct-gtttgcagGCAACACATGTTGCAGCGCAGTATGGCCAGACAGCATTTATTTATCATATTGTTGCGAAGTGGAATGCTGATCCAGATGTCCCTGATAATGATGGAAGAA
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G087806_T01 (Zea mays), 3'ss of exon 2
acatctgctaatttggtagtttgggattcttgttttacttgaagcacaagcgtgtggctgtaaatgttaattttactaattatgatttgctt--ggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
||| || | || || | |||| || |||||| | || | | | ||| | | | ||| ||| | ||| | ||| | ||||||||||| ||||| ||||||||||| || ||| |||||||||||||| |||||||||||||||| || ||| | ||||||||||||||||| |
tcatgtgattgttctgtgttaagggaaaaaaagaataattgaagt-tgattatgcaga-gaatttgtcacagctctttatttcgatatacttctgtgttcagGCCACGCATGTTGCAGCACAGTATGGTCAGACTGCATTCATTTACCACATTGTTGCAAAATGGAATGCTGATCCAGATATCCCTGATAATGATGGAAGGA
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G024437_T01 (Zea mays), 3'ss of exon 2
---acatctgctaatttggtagtttgggattcttgttttacttgaagcac-aagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
||| || | || | ||| |||| | | | | | || | | | ||| | ||| ||| || || ||| | || |||||||| ||||| ||||||||||| || ||| |||||| ||||||| | |||||||||||||| || ||| | |||||||||||||| || |
ttgtcatgtgattgttccat-gttagggaaaaaagaaccagtgaagttgttatgcagagaatttttcacagctctttaagtaaatatatttc---tgtgttcagGCCACACATGTTGCAGCACAGTATGGTCAGACTGCATTCATTTACCGCATTGTTGCGAAATGGAATGCTGATCCAGATATCCCTGATAATGATGGGAGGA
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------acatctgctaattt--ggtagtttgggattcttgttttacttgaagcacaagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
|||||| | || | || ||||| | || || | ||| ||| |||| ||||||| | ||||| ||| |||||| || |||| |||||||| ||||| ||||| ||||| ||||| |||| ||| |||| ||||| ||||||||||| ||||| || |||||||||||||||||||
gttcatatctcttctttaactacgcgtccatgttctctgctgacttctatcaaatttcccttcttttcttgtttagttctcaa-----tgggtgta--tgttaatact--taattttgaactgcttg----tagGCAACACATGTTGCCGCACAGTATGGCCAGACTGCTTTTCTTTGTCACGTTGTCTCAAAGTGGAATGCTGATCCTGACGTGCCTGATAATGATGGAAGAA
upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
--acatctgctaatttggtagtttgggattcttgttttacttgaagcacaagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
|| | || || || || | | ||| | || | | || | | || ||||| || ||| | | || |||||||| |||||||| |||||||||||||| || |||||||| |||||| ||||| |||||||||||||||| ||||||||||||||||||||||||||||
attcaatt-ttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatttactctct-ctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
tactaat putative branch site (score: 1)
tttgctt putative PPT
tgtaaatgttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatctgctaatttggtagtttgggattcttgttttacttgaagcacaagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
-catctgc
- - - - - - - - - gtttggg
- - - - - - - - - - - - - - - - - - - - - - cacaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg