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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtctttttctaaacacactttctctgttgattttatgggtttgcttttgagtcatgggactactttatcactgcaatcaaggtggttaccctttcattattatctgatcacaagtactttttactttctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCATGGTTTACTGGTGAGGCTATGGAAGCAGAGGATTTTGAAATAGATGACGATGAGGAAGAT

Basic information

species Arabidopsis thaliana
transcript AT4G26110.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26110.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S340_43V6.2 (Physcomitrella patens), 3'ss of exon 10
gttcgtctttttctaaacacactttctctgttgattttatgggtttgcttttgagtcatggg-actactttatcactgcaatcaaggtggttaccctttcattattatctgatcacaagtactttttacttt-ctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCATGGTTTACTGGTGAGGCTATGGAAGCAGAGGATTTTGAAATAGATGACGATGAGGAAGAT
                                       |  ||   |   ||| || | || | | || | |      ||||     |  | || |    ||  | |    ||||| |   |||||||  |  ||||| || || ||| |||| ||||||||||||| |||||| || |||||||| || |||||| || |||  ||||||||||||   |||||||| || |  || 
---------------------------------------tctgtaaacaagtgattcttaggtatttctctgtttacagaatcgtctagtgttccatagacttggttttgtctcacacgggatttttaccctgttgcagGTCCACGATTAGGGACAAGATTATTCCTCATGCTGTTTCCTGGTTTACGGGAGAGGCTTTGCAAGGTGAGGATTTTGAAGATGATGACGAAGAAGGCGAC
















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|164003657|gb|ES000290.1|ES000290
EST:     GAGGATCTTCAAAACCTGATGGAACAAGATTATGACATTGG                         ATCTACTATTCGGGAAA-GATTATTCCTCGTGCTGTCTCATGGTTTACTGG
genomic: GAGGATCTTCAAAACCTGATGGAACAAGATTATGACATCGGgttcgtcttt ... ctttctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCATGGTTTACTGG
EST: gi|124976514|gb|EL049926.1|EL049926
EST:     GAGCTGAGGATCTTCAAAACCTGATGGAACAAGATTATGACATCGG                         ATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCA
genomic: GAGCTGAGGATCTTCAAAACCTGATGGAACAAGATTATGACATCGGgttcgtcttt ... ctttctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCA
EST: gi|164225571|gb|ES126315.1|ES126315
EST:     GAAAGAGCTGAGGATCTTCAAAACCTGATGGAACAAGATTATGACATTGG                         ATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCATGGTTTAC
genomic: GAAAGAGCTGAGGATCTTCAAAACCTGATGGAACAAGATTATGACATCGGgttcgtcttt ... ctttctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCATGGTTTAC
EST: gi|164061863|gb|ES049290.1|ES049290
EST:     CTGATGGAACAAGATTATGACATTGG                         ATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTC
genomic: CTGATGGAACAAGATTATGACATCGGgttcgtcttt ... ctttctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtggttaccctttcattattatctgatcacaagtactttttactttctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCATGGTTTACTGGTGAGGCTATGGAAGCAGAGGATTTTGAAATAGATGACGATGAGGAAGAT
                       atctgat  putative branch site (score: 4)
                                    tactttttactttct  putative PPT
             tttcattattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtctttttctaaacacactttctctgttgattttatgggtttgcttttgagtcatgggactactttatcactgcaatcaaggtggttaccctttcattattatctgatcacaagtactttttactttctgcagATCTACTATTCGGGAAAAGATTATTCCTCGTGCTGTCTCATGGTTTACTGGTGAGGCTATGGAAGCAGAGGATTTTGAAATAGATGACGATGAGGAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA