Sequence
atgc intronic sequence ATGC exonic sequence...tgtgcttgaagctctgctttgtatttataaatatgcctttgtatttatctcacattcttgtttgattaaatgccaacaagatttcgtgctgttgtggcagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGATTTTTTTCTTGCCGGGAGTTCTAGTGACGAAGCAGATGCGGATGATGAATGGAC
Basic information
species | Glycine max |
transcript | GLYMA20G35300.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35300.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G43720.1 (Arabidopsis thaliana), 3'ss of exon 4
---------tgtgct-tgaagctctgctttgtatttataaatatgcctttgtatttatctcacattcttgtttg--attaaatgccaacaagatttcgtgctgttgtgg-----cagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGATTTTTTTCTTGCCGGGAGTTCTAGTGACGAAGCAGATGCGGATGATGAATGGAC
|||||| | | ||||| | || | | | || | ||| || | | | | ||| | | | | | |||||||| ||||||| || ||||| |||||||||||| |||| || |||||||||||||| ||| | |||||||| || || |||||||| || |||||||||| |||
gtaaacacatgtgctatatatagatgcttatttgtttcccttttttccctggaactattaagtatcgtaggtcgtagctaataaaggatgatttatgctattgttgtggacaaacagAGACGGGGAGTGAAGATGATGGTCTTCTGGACCTTAGTGATGATGATTTCTTTGATAAAGGGAGTTCAAGCGATGAAGCAGACGCAGATGATGAATTGAC
upper sequence: GLYMA20G35300.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G04230.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------------tgtgcttgaagctctgctttgtatttataaatatgcc---tttgtatttatctc-----acattcttgtttgattaaatgccaacaagatttcgtgctgttgtgg--cagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGATTTTTTTCTTGCCGGGAGTTCTAGTGACGAAGCAGATGCGGATGATGAATGGAC
| || ||| | ||||| || | || || || | || | | || || || || | || | ||| || | || ||||||| || || || ||||||| ||||||||| |||||||| ||||| || ||| | ||| ||||| |||||||||||||||||||||||||| |||||
gtaatgatgatatgtggagatgtttatatgggtcctttttcccttgaatttctgtttaaaatttggggcagcgtgcttttttttgtcattgcatgcattccgaccttctgttggcttttgaaaaaatactgattatgttgatcattaatattttttggttcgtgtgaaaaacagAGACAGGGAGCGAAGATGATGCTCTTTTGGACCTGAGTGACGATGACTTCTTTGTCAACGGAAGTTCAAGTGACGAAGCAGATGCGGATGATGAGTGGAC
upper sequence: GLYMA20G35300.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g04640.t01 (Vitis vinifera), 3'ss of exon 4
tgtgcttgaagctctgctttgtatttataaa-tatgccttt-gtatttatctcacattcttgtttgattaaatgccaacaagatttcgtg---ctgttgtggcagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGATTTTTTTCTTGCCGGGAGTTCTAGTGACGAAGCAGATGCGGATGATGAATGGAC
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-----aataaactattgttaacagaaaaaacctacagttttagtggctgggtggactttttctgtgctcactagactgatggactttttggacttcccttaacagAGACAGGGAGTGAAGATGATGGGCTTTTGGATCTGAGTGAGGATGATTTTTTCTTAAGTGGAAGCTCTAGTGATGAAGCAGATGCTGATGATGAATGGACMapped 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|37995190|gb|CF806779.1|CF806779EST: GATTGAAGATAGGTTGGTTGCAGCTGCTGCAAGTGGCAAGGATTTAGAAG AGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGANNNNN
genomic: GATTGAAGATAGGTTGGTTGCAGCTGCTGCAAGTGGCAAGGATTTAGAAGgttcattatt ... gttgtggcagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGATTTTT
EST:
gi|193521200|gb|FK480311.1|FK480311EST: GATTGAAGATAGGTTGGTTGCAGCTGCTGCAAGTGGCAAGGATTTAGAAG AGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGA
genomic: GATTGAAGATAGGTTGGTTGCAGCTGCTGCAAGTGGCAAGGATTTAGAAGgttcattatt ... gttgtggcagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctcacattcttgtttgattaaatgccaacaagatttcgtgctgttgtggcagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGATTTTTTTCTTGCCGGGAGTTCTAGTGACGAAGCAGATGCGGATGATGAATGGAC
ttgtttgattaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgcttgaagctctgctttgtatttataaatatgcctttgtatttatctcacattcttgtttgattaaatgccaacaagatttcgtgctgttgtggcagAGACTGGCAGTGAGGATGATGGTCTTTTGGATCTGAGTGATGATGATTTTTTTCTTGCCGGGAGTTCTAGTGACGAAGCAGATGCGGATGATGAATGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- tgcttga
- - - - - -ctctgct
- - - - - - - - - - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcgtgc