Sequence
atgc intronic sequence ATGC exonic sequence...atatattattatttatattcattagcataattttgaactccctattttctctgtggcttgaattaggccctatgtccttaatagattattattttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
Basic information
species | Glycine max |
transcript | GLYMA18G06190.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 2
---------------atatattattatttatattcattagcataattttgaactccctattttctctgtggcttg-aattaggccctatgtccttaatagattat-tattttgt-aggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
| | ||| || || || | |||| ||| | |||| || | || | | |||| | | | || | ||| | ||||| || ||| | | | ||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||| | || || ||
ggttcataaaaagttgagcagcaaagtttttaccagtt--caagagtttgtactgttaaatttcactatagcaagcgaataggattcctcttgcttatgcagTATGTGTTTTGCCAGAAATTGCATACAGTTGGCCAATACTTCTTGGTGGGCAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATTTCTATTAGTAG----------------
upper sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 2
atatattattatttatattcat-tagcataattttgaactc-cctattttctctgtggcttgaattaggccctatgtccttaatagattattattttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
|| | |||||||| | | | | | | || | | || | | | | | ||| | |||| || | ||| | | || | ||| |||| | | ||||| || ||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| | || || ||| | ||||| || ||
attt-ttattattgaagtccttacaaggtcatgtcgttctagtgtttctatttctttgctaccagtaggaccctctcctgatatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA-
upper sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G027043_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------atatat-tattatttatattcattagcataattttg-aactccctattttctctgtggcttgaatt-----aggccctatg------tccttaatagattat-tattttgt-aggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
||||| || | | | |||| | | | | || || | | | | ||| || ||| ||| | ||| | ||| | | | ||||| ||| |||| | ||||| || ||||| ||||| |||||||| ||||||||||| ||||| ||||| ||||| | || || ||| | ||||| || ||
gtaagttgcttggttggatcgtctttttttgctcttgtgctaatgtgctgtttaatttgctactgttgatatagataatgtgtgtattaaatggattggccttacaaggtcatgtcattctagtgctttctatttctttgctacctgtaggaccctccctgatatacagtgtgttttgccagGTATAGCATACCGTTGGCCAATTCTTCTCGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA-
upper sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
-------------atatattattatttatattcattag---cataattttgaactccctattttctctgtggcttgaattagg---ccctatgtcc---ttaatagattattattt-tgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
| | | | ||||||| | | || | | |||| | | | || || | | | || || | || || || | |||| ||| | |||| || ||| |||||||| || ||||||||||| |||||||||||||||||||| ||||||||||| |||||| | | ||| | || ||||| | ||
gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA-
upper sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
------atatattattatttatattcattagcataattttgaactccctattttctctgtggcttgaattaggccctatgtccttaatagattattattttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
| || | | | | ||| | | || || | || | || ||| || || | |||| | || | | ||| |||||||||||| | | |||||| | ||||||||||| ||||||||||||||||| |||||||||| ||| |||||| | || ||||| | |||||||| ||
gaacacctgcatgtgggcccacagctttgtgtatattctgagcctgtggatctgctttatgctttg--ccag---ctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA-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|20449042|gb|BQ253166.1|BQ253166EST: TTTTGGCTTAAACTTCGATGTGGTTTAGCAGCTCCAGCCTTGAACACAAG AATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGT
genomic: TTTTGGCTTAAACTTCGATGTGGTTTAGCAGCTCCAGCCTTGAACACAAGtaattgactt ... attttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGT
EST:
gi|209727492|gb|BW651961.1|BW651961EST: TTTTGGCTTAAACTTCGATGTGGTTTAGCAGCTCCAGCCTTGAACACAAG AATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAC-CTCATTGGACAGT
genomic: TTTTGGCTTAAACTTCGATGTGGTTTAGCAGCTCCAGCCTTGAACACAAGtaattgactt ... attttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctctgtggcttgaattaggccctatgtccttaatagattattattttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
ccttaat putative branch site (score: 4)
ttatttt putative PPT
ttaatagattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatattattatttatattcattagcataattttgaactccctattttctctgtggcttgaattaggccctatgtccttaatagattattattttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtc