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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaacctttctctgttttctcaataagtttagatttttttctgcgtgtgtgattctaatgatacactacattaatgttatcag

Basic information

species Arabidopsis thaliana
transcript AT3G49470.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49470.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G40550.1 (Glycine max), 5'ss of exon 3
GCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaacctttctctgtt-ttctcaataagtttagatttttttctgcgtgtgtga-ttctaatgatacactacattaatgttatcag
|||||| |||||||| ||||||||  | || || ||||||||||| ||  |||||||||| |||||||||||| | || || ||||||||||| ||||| || |  | || | | || || |   | | | |    | | |      ||  ||  ||||||    | | ||  ||| ||  || ||
GCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatatattattgttctttactgtgatctatctggaagatggatggcttctaac--caaattatttta-tgc-attag

upper sequence: AT3G49470.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G14250.1 (Glycine max), 5'ss of exon 3
GCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaacctttctctgttttctcaataagtttagatttttttctgcgtgtgtgatt-ctaatgatacactacattaatgttatcag
|||||| |||||||| ||||||||| | || || ||||||||||| ||  | ||||||||||| ||||||||| | || || ||||||||||| ||||| || |  | || | ||| || |   |   ||  |   | | ||||   |   |||  ||  | |  || |   || |||  || ||
GCAGAGCAGAAGTGAGAAGAAGAGTCGAAAAGCAATGTTGAAGCTGGGACTAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatatgtattattgttcttttctgtgatctatctggaagatggatggcttttaacccaattgttttatgc-attag

upper sequence: AT3G49470.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 5'ss of exon 3
GCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaacctttctctgttttctcaataagtttagatttttttctgcgtgtgtgattctaatgatacactacattaatgttatcag
|||||| |||||||| ||||||||  | ||||| |||||||||||||| |||||||| || ||||||||| |  | || ||||| |||||||| ||||| |||||  ||| |||| |||||      || |  | || | ||    ||  || |  |  |   |   |    |    ||  |||
GCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCACCATTAAGAGAACAAAAAATgtaaaattttgtctgatttctgttcttgtattcacttgtatc---atgaatgttctt--taccagtttttcctgggcttggcag

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|124900842|gb|EH975460.1|EH975460
EST:     GAACGAAAAAC                         GTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
genomic: GAACGAAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
EST: gi|164203045|gb|ES090296.1|ES090296
EST:     GAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAAC                         GTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
genomic: GAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
EST: gi|116418723|gb|EG461315.1|EG461315
EST:     TGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAAC                         GNNNNNNNCTTTATCTTTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
genomic: TGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
EST: gi|164164446|gb|ES161470.1|ES161470
EST:     TGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAAC                         GTTCTCTTCTTTATCTCTAAGCC
genomic: TGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCC
EST: gi|164058623|gb|ES154450.1|ES154450
EST:     GAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAAAC                         GTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGA
genomic: GAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACG-AAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGA
EST: gi|124851816|gb|EH936253.1|EH936253
EST:     TAACCATCAAGAGAACGAAAAAC                         GTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
genomic: TAACCATCAAGAGAACGAAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
EST: gi|86083906|gb|DR379665.1|DR379665
EST:     CCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAAC                         GTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
genomic: CCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
EST: gi|116418728|gb|EG461320.1|EG461320
EST:     TGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAAC                         GTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA
genomic: TGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaaccttt ... atgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaacctttctctgttttctcaataagtttagatttttttctgcgtgtgtgattctaatgatacactacattaatgttatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA