Sequence
atgc intronic sequence ATGC exonic sequencegtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
Basic information
species | Glycine max |
transcript | GLYMA11G35640.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 6
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttt-tttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
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--------------------------------------------------gtaatgctttgaacataactccctaaattgtttccttg--tgcttg------tcat-tagttgatataaaacatttgtttcttccccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G303752_T03 (Zea mays), 3'ss of exon 6
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtg-tggttaaaatg--ttttttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
| | || | ||| | | ||| | | | ||| || | || | ||| | ||| | | ||||||||||| ||||||||||| ||||||||||||||||||| || || || || || | | || |||| ||||| |||| || | |||||||||
---------------------------------------------------------gttatattctgctcttccctccctaaatttgaatctcatgttcaggcatcagctgatagtaaggatgcatgtttgttcatccagTATGATCCACCTCAAGATCCCAACGTTTTCATACATAGAGCTGGCCGTACAGCACGCTATGATCAAGAAGGGGATGCTATTGTTTTTCTCTTACCAAAG
upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0067g01900.t01 (Vitis vinifera), 3'ss of exon 6
gtagctctgtgcttctgtgaccttgtatatgatactgtct--attgactattgcatttcat-cttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
| |||| | ||||| || || | | | || | ||| | | | ||||| | ||| || ||| || | || | ||||| ||||||||||||| |||||||||||||| || |||||||| ||||| ||||| ||||||||| |||| | |||||| ||||||||| || |||||||||||
------------------------------tacactggcaggattgaacat---atctaacacatcatacattccccatttatctcctgtttctga-aagctaggtgatgattttctgtc-------tgcttcttatgcagTATGATCCCCCTCAAGATCCAAATGTCTTCATACACAGAGTTGGTCGGACTGCTCGGATGGGCAGACAAGGAAGTGCTGTTGTTTTTCTATTACCAAAG
upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ12594 (Selaginella moellendorffii), 3'ss of exon 5
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtg-cagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
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--------------------------------------------------------------------------gtatttgaaaccttatcatgatatgtggttttataacatcgtt-----gttctttcgcgtgacagTATGATCCTCCCCAAGACCCAAACGTTTTCGTTCATAGGGTCGGCCGAACTGCCAGAATGGGAAGAGCGGGAGATGCTTTAGTTTTTCTTCTTCCAAAG
upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ23182 (Selaginella moellendorffii), 3'ss of exon 6
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
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---------------------------------------------------------------------gtaaacgctttgtgataaaagttttgaggctcgcttcgtaacacagt-aatttgagtcatcttgtccagTATGATCCTCCTCAAGATCCAAACACGTTTGTTCATAGAGTCGGGCGTACTGCAAGAATTGGACGCGTTGGCCATTCTGTTGTGTTCCTTCTTCCAAAG
upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ25181 (Selaginella moellendorffii), 3'ss of exon 6
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
|| | | | | | | | || || || | |||||| ||||||||||||||||||||||||||| || | |||||||| || || ||||| | | || || ||| ||||||| ||| | | ||||||
---------------------------------------------------------------------gtaaatgctttgtgataaaagttttgaggctcgcttcgtaacacagt-aatttgagtcatcttgtccagTATGATCCTCCTCAAGATCCAAACACGTTTGTTCATAGAGTCGGGCGTACTGCAAGAATTGGACGCGTTGGCCATTCTGTTGTGTTCCTTCTTCCAAAG
upper sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ10195 (Selaginella moellendorffii), 3'ss of exon 5
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtg-cagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
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--------------------------------------------------------------------------gtatttgaaaccttataatgatatgtggttttataacatcgtt-----gttctttcgcgtgacagTATGATCCTCCCCAAGACCCAAACGTTTTCGTTCATAGGGTCGGCCGAACTGCCAGAATGGGAAGAGCGGGAGATGCTTTAGTTTTTCTTCTTCCAAAGMapped 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|193377674|gb|FK343214.1|FK343214EST: ACCGGGTGTAGATTGTATAGTGCAG TATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACT
genomic: ACCGGGTGTAGATTGTATAGTGCAGgtagctctgt ... tcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACT
EST:
gi|208318761|gb|GE111508.1|GE111508EST: CCGGGTGTAGATTGTATAGTGCAG TATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACT
genomic: CCGGGTGTAGATTGTATAGTGCAGgtagctctgt ... tcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
tgctaaa putative branch site (score: 2)
tgttttttctt putative PPT
ttaaaatgttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttttttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT