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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagaaagatcatacattacatttttgtacaagctctatgattgttcaaaacttacattttcttcttctttttttcatatattgaagCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAG

Basic information

species Arabidopsis thaliana
transcript AT5G01220.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01220.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 6
------gtgaagaaagatcatacattacatttttgtacaagctctatgattgttcaaaacttacattttcttcttctttttttcatatattga----------------agCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAG
       ||   | | ||  |    |   |||||       |  | | ||| |   | | || ||  ||||| | || ||    || ||||                  ||| ||| |  | || |||||||| |||||||| ||||||||||||||| ||||||||||||||  | | |||||||||  ||| || | 
gttgtcatggctatacatagttttgtttttttttacctttaccatcttattctgacatagtttcaccttcttttgctattaccaatttattatgatgggtcatatttccagCCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC

upper sequence: AT5G01220.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G100652_T03 (Zea mays), 3'ss of exon 5
gtgaagaaagatcatacattacatttttgtaca-agctctatgattgttcaaaacttac-attttcttcttctttttttcatatattga-agCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAG
||  |   |  | |||   ||  | | | |    || |   || |  |   ||   ||| || |   |||       | ||||| ||   ||| ||| || | || |||||||| |||||||| || |||||||||||| |||| ||||||||       |||||||||  ||| || | 
gtttacttaactaataacctatctatgtatctgtagtttcttgttcttgttaattgtaccatatatctctcaaacggtgcatatgtttccagCCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAAC
















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|116431123|gb|EG473715.1|EG473715
EST:     TCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG                         CTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATC
genomic: TCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAGgtgaagaaag ... tatattgaagCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATC
EST: gi|86057508|gb|DR353265.1|DR353265
EST:     TCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG                         CTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATC
genomic: TCCTTCTGCTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAGgtgaagaaag ... tatattgaagCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATC
EST: gi|163996231|gb|ES114807.1|ES114807
EST:     CTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAG                         CTAATCAACTTCGACTTTGGAATAAAGGGTGTCGATTCAGAAAGCTTCAAT
genomic: CTGCCATTGGAAAAGATCTTATAGCAGCTGGTGCAACTGCAGgtgaagaaag ... tatattgaagCTAATCAACTTCGACTTTGGAATAA-GGGTGTCGATTCAGAAAGCTTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctatgattgttcaaaacttacattttcttcttctttttttcatatattgaagCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAG
                 aacttac  putative branch site (score: 2)
                   cttacattttcttctt  CT-rich tract
                        attttcttcttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagaaagatcatacattacatttttgtacaagctctatgattgttcaaaacttacattttcttcttctttttttcatatattgaagCTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA