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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCACAATGCAATTCCAGCTTTGCACTGTCTTTTTCACATTTTCCTTGGGTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgtttgtctgcctactctatgctgtctctttctgtacttgtcttctgaaatgttaatctgtttatttgtcaacag

Basic information

species Glycine max
transcript GLYMA20G38860.1
intron # 46
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 46
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 10
TGTCACAATGCAATTCCAGCTTTGCACTGTCTTTTTCACATTTTCCTTGGGTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgtttgtctgcctactct------atgct-gtctctttctgtacttgtcttctgaaatg--ttaatctgtttattt---gtcaacag
|||| ||||| ||||| |||||| |||| ||||| || || ||| |||||||||| || || |||||||| || ||||| || ||||||||||||| ||| | | | | ||||| ||| ||||| | || | |||| | || | || ||||| || | | |||
CATCACGATGCAGTTCCAACTTTGCTCTGTATTTTTTACTTTCTCCCTGGGTACAAGGACCCACTATTTTGGCCGCACAATACTACATGGTGGTGCAAAGgtagggtcctttgtttttaagtgatgcttatctacttctg-atttttactctgtattgatctgatgtgtttcttctggattaccag

upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 46
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 5'ss of exon 43
TGTCACAATGCAATTCCAGCTTTGCACTGTCTTTTTCACATTTTCCTTGGGTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgtttgtctgcctactctatgctgtctc-tttctgtacttgtcttctgaaatgttaatctgtttatttgtcaacag
| ||||||||||| ||||| || |||||||| |||||||||||| | ||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| | | | | ||| | || | |||||| | || || ||||| | || ||||| |||||
CATAACAATGCAATTTCAGCTATGTACTGTCTTCTTCACATTTTCCCTTGGTACAAGAACCCATTATTTTGGACGGACAATTCTCCATGGTGGTGCAAGGgtatattctcattctcggttctaaaaaatctctgtaa--attttttggaatgtgataaccattgtttgttaacag

upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 46
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 41
TGTCACAATGCAATTCCAGCTTTGCACTGTCTTTTTCACATTTTCCTTGGGTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgtttgtctgcctactctatgctgtctctttc---tgtacttgtcttctg--aaatg-ttaatc--tgtttatttgtcaacag
|||||| ||||| || ||||| || ||||||| ||||| ||||| |||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||| ||| || | | || || | || || | | || ||||| | || | |||| |||| || ||||
TGTCACTATGCAGTTTCAGCTCTGTTCTGTCTTCTTCACTTTTTCTCTGGGCACAAGAACACATTATTTTGGTCGGACTATTCTTCATGGGGGTGCAAGGgtttgttctcctgcttcctttttccttgatcaattatatttttagtatggaaaatgatcaaccgttgttaatttctcgacag

upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 46
lower sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 42
-TGTCACAATGCAATTCCAGCTTTGCACTGTCTTTTTCACATTTTCCTTGGGTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgt-------ttgtctgcctactctatgctgtctctttc-----tgtacttg-tcttctgaaatgtt--aatctgt---ttatttgtcaacag--------
||| |||||||| || ||| | | || ||||| |||||||||||||| ||| |||| ||||| || || || ||||| |||||||| ||||| | ||| | | | | | ||| || || | | | || | | || | ||| || || | |||| | | ||
CTGT-ACAATGCAGTTGCAGTTGGCTTCAGTGTTTTTTACATTTTCCTTGGGAACACGAACTCATTACTTCGGGCGCACAATCCTTCATGGAGGTGCTAAGgtaccaaagtccttggtgttcgttatagtgcatcgtctaaaaatatgctcggttttatcaaactttcagattcatgttttatggtttgagagagagagag

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|254331761|gb|GR843611.1|GR843611
EST:     GTACAAGAACACATTATTTTGGTCGGACCATTCTTCATGGTGGTGCAAGG                         TATCAAGCAACTGGCCGCGGTTTTGTTGTCCGCCATATCAAATTTTCAGAG
genomic: GTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgtttgtctgc ... ttgtcaacagTATCAAGCAACTGGCCGCGGGTTTGTTGTTCGCCATATCAAATTTTCAGAG
EST: gi|298188356|gb|HO035049.1|HO035049
EST:     GTACAAGAACACATTATTTTGGTCGGACCATTCTTCATGGTGGTGCAAGG                         TATCAAGCAACTGGCCGCGGTTTTGTTGTCCGCCATATCAAATTTTCAGAG
genomic: GTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgtttgtctgc ... ttgtcaacagTATCAAGCAACTGGCCGCGGGTTTGTTGTTCGCCATATCAAATTTTCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCACAATGCAATTCCAGCTTTGCACTGTCTTTTTCACATTTTCCTTGGGTACAAGAACACATTATTTTGGTCGGACAATTCTTCATGGTGGTGCAAGGgtttgtctgcctactctatgctgtctctttctgtacttgtcttctgaaatgttaatctgtttatttgtcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG