Sequence
atgc intronic sequence ATGC exonic sequence...gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
Basic information
species | Glycine max |
transcript | GLYMA15G04470.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g38550.2 (Oryza sativa), 3'ss of exon 4
-----gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
|||| | ||| | ||| | ||| | | || | | | | ||| | ||| || | || || | || | ||||||||| || |||||||| | || ||||| |||||||| |||||||| |||||||| |||||||||||| ||||||| ||
aattcattttggaggcttggcgcgcacttatcagtgtt-aatttggaagatttgtggtcaatta---ttttcttgctaaattattttgtgcttg-taacttgcagGTTGAAAGTATAGTTCTGAGCATCATTTCGATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAATATTGAAGCGGCT----------------------
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 2
gtttttgccacttcttgtccaccacttgtggtttgacatacta-gttgtaaagctatttaaaacctg---cttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
| || | | | |||| | | ||| | ||| | || | |||| ||| | | || | | | | | | || ||||| ||||| ||||| | || ||||| |||||||||||| |||| ||||||||||| ||||||||| ||||||| ||
---tatgtttatcttctctagctttttgtaagtagccattttttactgtctaatcatcatattcctgattcttgtaattttaatgagtgttttccat-ttacagGTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCT----------------------
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
-gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtct-tgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
||| || || ||||| | | ||||| | ||| || | || | | ||||| | ||||| | | | | | | ||||||| || |||||||| | || ||||| || ||||| |||||||| ||||| || |||||||||||| ||||||||||
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgcttt--agttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC----------------------
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 4
gtttttgccacttcttg-tccaccacttgtggtttgacat--actagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
| || | || | | || || | || | | | | | | || || | | | | | || | ||||| ||||||||||| || ||||| | || || ||||| ||||| |||||||| |||||||| ||||||||||| |||| || ||
-gcctagcttccactaggtacatagagaatgatctgtcttgaatgaacactgctgtatgatatcactagttgttaagctgatgattgttatgca--tttgcagGTAGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAACATTGAGGCAGCT----------------------
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 4
gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
| || | || | || | ||| | || | | | ||| | | ||| | | || || ||| | | | ||||| || |||||||| || |||||||||||||||||||| || |||||||||||||| || ||||| ||||||||||
atattatagagtttaaggtcatcgtgtgttgacaattattttccctatctagcgaccatattaatgcacttacaactattgcattgatgttatgtcacagGTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA----------------------
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
gtttttgccacttc--ttgtcc-accacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
||| || || |||| | | ||||||||| | | || | | | |||| | || ||||||| | | ||| | || || ||||| || || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| |||||||||||||||||
-ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaacta-actatg-gttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT----------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|254336753|gb|GR842932.1|GR842932EST: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACA GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
genomic: ACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATACAgtatgtataa ... tgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
aattaat putative branch site (score: 3)
ctgtctt putative PPT
tatttaaaacctgctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttgccacttcttgtccaccacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC