Sequence
atgc intronic sequence ATGC exonic sequence...atgatttttatttacaacaatggggaagggagggacttggtttagattttgttgactggagaattgtggtaagtgaatggctttttttgtttgggtgcagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
Basic information
species | Glycine max |
transcript | GLYMA01G22470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G22470.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G25570.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------atgatttttatttacaacaatggggaagggaggg-------acttggtttagattttgttgac-----tggagaattgtggtaagtgaatggctttt-----tttgtttgggt-gcagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
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gtacgtcaagttaaggatactcactgttgtttgatggattgcaacatcatgggtttcttgatttgattggagttctgataatagctttgagaaaaactggtctgtggcatatttttgactctctgtttgttttacagTGACTGCTATGAAAGCATTGAAGGATTCACTACGTGTTCCTGATAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAGCTGGGACGCTTGGGAGGG
upper sequence: GLYMA01G22470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g03060.t01 (Vitis vinifera), 3'ss of exon 2
atgatttttatttacaacaatggggaagggagggacttggtttagattttgttgactggagaattgtggtaagtgaatggctttttttgtttgggtg--cagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
||| |||| | | || || | || | || | | | |||| | ||| | || || | || | ||||| |||| |||| ||||||||| || || |||| | || | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
atgtattttgtcaatgtgaaaccaatgggtcctaataatgtgggaaaccctttattttgcaa--tgtgatgtgtggtttaattattgggcatgtttctccagTGATTGCTATGAGAGCATTGAAAGAATCTCTTCGTATTCCGGCTAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
upper sequence: GLYMA01G22470.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ07666 (Selaginella moellendorffii), 3'ss of exon 1
atgatttttatttacaacaatggggaagggagggacttggtttagattttgttgactggagaattgtggtaagtgaatggctttttttgtttgggtgcagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
| || | ||| | ||| || || |||| | | ||||||| ||| |||||| | || ||| ||| ||||| || || ||||| ||||| |||||||| |||||||| |||||||||||||| |||||||||| | ||||| ||
-------------------------------gtatgttaaaggaagtttcg--gacgtgatgttt---gtaaacgttt--ttttttttttttttttgcagTTCTAGCAATGCTAGCTTTGAAAGAAAGCTTGCGAGTTCCTGAGAGAATGGGATGGAATGGCGATCCTTGTGCTCCGTTTAATTGGGATACATGGGAAGG
upper sequence: GLYMA01G22470.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ07722 (Selaginella moellendorffii), 3'ss of exon 1
atgatttttatttacaacaatggggaagggagggacttggtttagat-tttgttgactggagaattgtggtaagtgaatggctttttttgtttgggtgcagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
| | | | | | || ||| ||||| || | || | | | | ||||||| ||| |||||| | || ||| ||| ||||| || || ||||| ||||| |||||||| |||||||| |||||||||||||| |||||||||| | ||||| ||
-------------------gtatgttaaaggaagtttcggacgtgatgtttgtaaac----gtttttttttttttttttttttttttttttttttttgcagTTCTAGCAATGCTAGCTTTGAAAGAAAGCTTGCGAGTTCCTGAGAGAATGGGATGGAATGGCGATCCTTGTGCTCCGTTTAATTGGGATACATGGGAAGGMapped 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|207805274|gb|GD777280.1|GD777280EST: TGATCCTTCCACTGTTCCAGAACAAG TGGTTGCCATGAAGGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGG
genomic: TGATCCTTCCACTGTTCCAGAACAAGgtgagtgggt ... ttgggtgcagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgttgactggagaattgtggtaagtgaatggctttttttgtttgggtgcagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
tgttgac putative branch site (score: 3)
ctttttttgttt putative PPT
tttttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgatttttatttacaacaatggggaagggagggacttggtttagattttgttgactggagaattgtggtaagtgaatggctttttttgtttgggtgcagTGGTTGCCATGAAAGCATTGAAGGATTCATTTCGAGTACCTGAAAGAATGGGTTGGAATGGTGATCCTTGTGCTCCTACTAATTGGGATGCTTGGGAGGG
- - - - - - - - - - - - - -gggaggg
- - - - - - - - - - - - - - - - - - - - - - - - -tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgg