Sequence
atgc intronic sequence ATGC exonic sequenceGGCACAGAGACAATTGATGTTACTGATGCGGTTGGATCCAATATTCGAATTGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGGttagattctcatggaaatgttttgttgaactgtttgggatttctgaggcttcaatttgctttgtggtttttaaaattatttaatttctgcaagaaaaact...
Basic information
species | Glycine max |
transcript | GLYMA18G04730.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G04730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 5'ss of exon 3
-GGCACAGAGACAATTGATGTTACTGATGCGGTTGGATCCAATATTCGAATTGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGGttagattctcatggaaatgttttgttgaactg------tttgggatttctga-ggcttcaatttgctttgtggtttttaaaattatttaatttctgcaagaaaaact
||||| || || ||||||||||||||||| || || || || ||| || |||| |||||||| |||||||| ||||| || ||||| ||| | ||||||||| | || | | | | | |||| | || | | ||||| || || || | | || | | | | | |||| || | |
GGGCACTGAAACTATTGATGTTACTGATGCAGTAGGTTCAAACATTAGAGTTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAGgttcgcttattgtccacttctgttgtaaatttgacttattctatgatttttgctggtaatgatctacattaggatcatcgga-tcatttggttgtggtcat-------
upper sequence: GLYMA18G04730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 3
-GGCACAGAGACAATTGATGTTACTGATGCGGTTGGATCCAATATTCGAATTGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGGttag---attctc-----atggaaatgttttg----------ttgaactgtttg-ggatttctgaggcttcaatttgctttgtggttt----ttaaaattattta------------atttctgcaagaaaaact-----------------------------------------------------------
||||||||||| ||||||||||||||||| || |||||||| || ||||||| ||||||||||||||||| |||||| ||||||| ||| | ||||||||| | |||||| || | ||||| ||| |||| | || | | | | || ||||| ||||| | || | | ||||| || | || | ||| |
GGGCACAGAGACTATTGATGTTACTGATGCAGTGGGATCCAACATAAGAATTGACAGCAGAGGACCTGAAGTTATGCGCGTTGTTCCACGTCTCAATGAGgttggtttattctccatttctgttacaattttgacttttgtgtttgttttgttggtggggtattcatgtgtcctaatgcttcgtggtgtatcattgacttcatttagtccgcttctatatctttgataaaaaggttattatcatataaattatgtcaatatgtttagttaacaccactttccctgttcattgcag
upper sequence: GLYMA18G04730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G145854_T01 (Zea mays), 5'ss of exon 3
-GGCACAGAGACAATTGATGTTACTGATGCGGTTGGATCCAATATTCGAATTGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGGttagattctcatggaaatgttttg----ttgaactgtttgggatttctgaggcttcaatttgctttgtggtt-----tttaaaattatttaat--ttctgcaagaaaaact------------------------------------------------------------------------
||||| ||||| ||||||||||||||||| || || ||||| || || |||| ||||||||||||||||| |||||||||||||| || | ||||||||| | || | | | | |||| ||| | | || | ||| | | |||| | | | || || | || |||| || || || ||| | | |
AGGCACCGAGACCATTGATGTTACTGATGCAGTGGGGTCCAACATAAGAGTTGACAGCAGAGGACCTGAAGTTATGCGCATTGTTCCACGCCTCAATGAGgtttgtttattctccatttattttacaatttggatttttgtgtttttttttgtattcatgtgacctactgcttcgctatgtatcattagttcatcattttgctattctatatctttgagaaaccaaagattattatgttaatatgtttagtgaacatcacttttcctttttcttttccttgcag
upper sequence: GLYMA18G04730.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 5'ss of exon 3
-GGCACAGAGACAATTGATGTTACTGATGCGGTTGGATCCAATATTCGAATTGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGGttagattctcatggaaatgttttgttgaactgtttgggatttctgaggcttcaatttgctttgtggtttttaaaattatttaatttctgcaagaaaaact----
|| |||||||| |||||||| || ||||||||||| ||||| |||||||||||||||||||| ||||| || ||||| ||| | || ||||| |||||||| ||| | || | | || | | ||||| || | || ||||| ||| | | | ||| || ||||
GGGGACAGAGACCATTGATGTAACAGATGCGGTTGGTTCCAACATTCGAATTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAGgt-agactaagatc-acctaaattttatatctgttcttctttccaatcagtt---tttgcattgcatcctcccatagcattggcttcctgccttgtttctgcaacMapped 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|254341815|gb|GR852952.1|GR852952EST: TGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGG AGATAAATGAAGAATGGATTTCGGATAAAACCCGCTTTTGTTATGATGGTT
genomic: TGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGGttagattctc ... ccattgcaggAGATAAATGAAGAATGGATTTCGGATAAAACCCGCTTTTGTTATGATGGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCACAGAGACAATTGATGTTACTGATGCGGTTGGATCCAATATTCGAATTGATAGCAGAGGACCTGAAGTGATGCGCATTGTTCCTCGTTTAAATGAGGttagattctcatggaaatgttttgttgaactgtttgggatttctgaggcttcaatttgctttgtggtttttaaaattatttaatttctgcaagaaaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaaa