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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacacttacttatttttcgatattaataatacaatgccagagttaaatgatagcaaaaataataccctattcttcgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG

Basic information

species Arabidopsis thaliana
transcript AT4G26910.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
gtatacacttacttatttttcgatattaataatacaatgccagagttaaatgatagcaaaaata-ataccctattctt----cgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG
      ||| ||  || ||  | || |  | |  |    | |  | |   | ||   |  |||| || |  | | ||     | ||  || | ||||||||||||||  || |||||  | |||||| |||| ||||| || ||||| || ||||| |||||||||||||||||||| || |||||| | |||||||
----gtactgaccaatcttgtg-tactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG

upper sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
gtatacacttacttatttttcgatattaa-taatacaatgccagagttaaatgatagcaaaaataataccctattcttcgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG
             |||||  |  | |||     | ||| ||    |    ||  |   |    |      ||| |  |  || | | |   |||||||||||   || |||||  | || ||| |||| ||||| || ||||| || ||||| ||||||||||||||||| || || |||||| | |||||||
------------gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatg--tggctggctaattatatttgttt-tggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG

upper sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
gtatacacttacttatttttcgatattaataatacaatgccagagttaaatgatagcaaaaataataccctattcttcgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG
   ||   || || |||  |  |   ||      |   |       |   ||||| |     | |||| || ||  | ||  ||  | | ||||||||||||  || || || ||||| ||  |||| |||||||| ||||| || |||||||| ||||||||||| ||| | |||||||| || |||||||
--gtatgttttctaattactgaagtatagactagctgggttttctctttttgatatcc----tcatacactttttatggtc-tccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

upper sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G46200.1 (Glycine max), 3'ss of exon 12
gtatacacttacttatttttcgatattaataatacaatgccagagttaaatgatagcaaaaataataccctattcttcgttatct--gtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG
             ||| |||    |||| | | | |    |    |    |     |    ||     | || | ||  |  |||   | | |||||||||| |  || || || ||||| ||  |||| |||||||| ||||| || |||||||| ||||||||||| ||| | |||||||| || |||||||
------------gtatgttttctaattactgaaatataaactagctgggctttctcctttgatttcctcatactttttatggtctccatgttagGCTGCTGTCAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

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|47828366|gb|CK118050.1|CK118050
EST:     TTTATGAAAAGCATGGAGTGAAGTTGGGGCTTATGTCTGGATTTATTAAA                         GCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGAC
genomic: TTTATGAAAAGCATGGAGTGAAGTTGGGGCTTATGTCTGGATTTATTAAAgtatacactt ... tctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGAC
EST: gi|164001796|gb|ES102314.1|ES102314
EST:     GAGTGAAGTTGGGGCTTATGTCTGGATTTATTAAA                         GCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAA
genomic: GAGTGAAGTTGGGGCTTATGTCTGGATTTATTAAAgtatacactt ... tctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccagagttaaatgatagcaaaaataataccctattcttcgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG
                                             tctgtctc  CT-rich tract
        ttaaatgatagcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacacttacttatttttcgatattaataatacaatgccagagttaaatgatagcaaaaataataccctattcttcgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT