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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag

Basic information

species Arabidopsis thaliana
transcript AT5G62790.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 9
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag----------------------
 || || |||||||| ||||| |||||||||||||| |||||  |||| ||||||||||||||||| |||   ||||||||||| ||||||||||||||||| |     |||| ||| |  |||  ||||  ||  | |  ||| | |   |||  |     | |   ||   |   |  ||| ||                      
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTATGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtat-----aaaccttatt--ctatgttatgtttactgcattttgatatccatatattcg-gatacaaatggatgaggaaccatagccatagcacctacaagttccag

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 9
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttg--ctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtata-acatgtatttgttttgt-tccacag----------
 || || |||||||| ||||| |||||||||||||| || ||  |||| ||||||||||||||||| |||   ||||||||||| |||||||||||||||||||    || |  |  |  ||  |   |||     |||     |  | | |  |   || | |   |||        | ||  | |||           
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTACGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtctaaatctaattctatgttatgttggttaccgcattttaatatccatatatttggatgcaaatggatgaggaaccatagtacctacaagctacaagtt

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 5'ss of exon 9
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag-------------------------------------
 || || |||||||| || ||| ||||||| ||||| ||||| ||||| |||||  | |||||||| |||  |||||||||||| ||| | ||||||||||| |   ||  |  ||| |  ||    |  |  ||     |||| | |     ||    || | |  | |||  | | ||  | |                                      
AGAAGTTATTGAAGCACACTATCTGTTTGGGGCTGAATATGATGATATTGAGATCATAATTCATCCACAATCTATCATACATTCTATGGTCGAAACACAGgt-taattgttatcttattgtcttggcttcttcttaatatgtttaagatgtcaaataccatcagaactgtttcatattttttagaagcggtttcttatgtcttctccacccctttctctccag

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag
 |||||||||||||| || ||||||||||||||||| ||||| || || || ||||| || ||||| |||   || ||||| |||||||| || ||||||||  |        | | ||    ||   |  | |    | | |    ||| | |                                
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgct--tcaacacacaactaacacagctagtcaaatacag-------------------------------

upper sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag
 |||||||||||||| || ||||||||||||||||| ||||| || || || ||||| || ||||| |||   || ||||| |||||||| || ||||||||  |        | | ||    ||   |  | |    | | |    ||| | |                                
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgct--tcaacacacaactaacacagctagtcaaatacag-------------------------------

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|164163268|gb|ES024308.1|ES024308
EST:     ATCATACATTCCATGATTGAAACACAG                         GATTCATCTGTGCTTGCTCAATTGGGTTGGCC
genomic: ATCATACATTCCATGATTGAAACACAGgtcttgctga ... tgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCC
EST: gi|164020276|gb|ES076441.1|ES076441
EST:     GTCATTCATCCTCAAAGTATCATACATTCCATGATTGAAACACAG                         GATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTAC
genomic: GTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctga ... tgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTAC
EST: gi|125003558|gb|EL075827.1|EL075827
EST:     CATCCGCAAAGTATCATACATTCCATGATTGAAACACAG                         GATTCATCTGTNCTTGCT
genomic: CATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctga ... tgttccacagGATTCATCTGTGCTTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG