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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagttaacttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC

Basic information

species Arabidopsis thaliana
transcript AT1G34020.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
cttagttaacttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatgg-tagaaacttattcgaacctaat--gtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
  |  |     | || |||  |  | |   ||| |     |    | |  |||||         |  ||| || |   | |  |   || || ||||   ||| | || ||     ||||||||||||| ||  |||| ||||| |||||||||||||| ||||| ||||||||||||||||| || || ||||| || || |
tatcatagcagtgcagacc--tgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaatttc-cagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 5
-cttagttaacttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacata-catggtagaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
     | ||  ||    |  || | |   |||      |   ||  |  |   | |  || ||   ||  || |       | || | |||| |||  | || | || || |  |||||||||| ||| ||  |||| |||||||| ||||| ||||| |||||||||||||| ||||| || ||||||||||| || || |
tggaggatatattttttataatctgttgttgccatgaccattactatttttatcgtggcagggcctaacattttctttttttcatctacctgcatt--gtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAATTCATATGCATCGGAAGATTTACAGCAGTCTCGTTCCAAGTTCTAGGCC

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
-------cttagttaac-ttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
        ||  || |  ||| |||   | | ||| ||||  | ||   |||   |||  ||    |  | |     | |||    |  ||||        | | ||| | |||||     ||||||||| ||| ||  | || |||||||||||||||||||| ||||||||||||||||| || || ||||||||||| || || |
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattg-----ttttcctgtcacatgttttc---cttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 5
--cttagttaactt-acaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaact-tattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
   ||  |   ||| |      |  | |   | |||  |  |||||  ||  | || |       |   ||| | |||  | |  ||||        | | ||| | |||||     ||||||||| ||| ||  |||| || || |||||||| ||||| |||||||||||||||||||| || ||||||||||| || || |
tatttgatctgcttgatgttataaattttcattcttcggcgcaaact-tgacgaacctgggcatgacttactattttcttatcacatgttttc---cttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCCGTTGGGACGAATCTAAGCCAATTCATATGCATCGGAAGATTCACAGCCGTCTCGTTCCAAGTCCTAGGCC

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G08700.1 (Glycine max), 3'ss of exon 5
-cttagttaac-ttacaaaccatttct-ctgtgcttaaggccaaaccgtgctgtacatacatggt-agaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
  |   | ||| | | ||| |||     || |  |   ||   |    | ||  ||||      | ||  ||| | ||     |      | ||  ||   ||| | || |||  |||||| ||||| || || ||||| |||||||||||||| || |||||||| || |||||||| ||||| || || ||||| |||||||
tgtggataaacatgataaatcatgagaactcttatgtcggttgacattttcttaacatttccattcagtgactgactcatctttg----tcttggttttgacagATTTTCATATTCCTGTCATGCACTATTGCAATTGGCACCAACCTAAGCCAATTTATCTGCATTGGCAGATTCACTGCTGTTTCTTTTCAAGTACTGGGAC

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 4
cttagttaacttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaacttattcga---acctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
    || || || |      |  || | | | ||        || |||| |   |   |   ||||   | |   |    |||  |   | ||  || ||||| | ||||||| ||| || || || || ||| | || |||||||| ||||||||||| ||||| || |||||||||||||| || || ||||| || || |
---ggtgaatttcctctagttcactttattcctagcattgtgccttgctatttgtctttacaagaatgatctctcacttgcctcgttgtcttggcttttgcagATATTTATAATCCTTTCATGTACTATCGCGGTAGGGACCAACCTCAGCCAGTTCATATGCATTGGTAGATTCACAGCTGTCTCCTTTCAAGTACTTGGCC

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|86075486|gb|DR371243.1|DR371243
EST:     GCTGACAGAAAAAAGAGTAGACATGTACGATTACAACTTGGTTTCAGTG                         CTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAG
genomic: GCTGACAGAAAAAAGAGTAGACATGTACGATTACAACTTGGTTTCAGTGgtaagtacga ... aattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgtacatacatggtagaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
                               acctaat  putative branch site (score: 3)
                   aaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttagttaacttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - -caaacca
- - - - - - - - - - -ttctctg
- - - - - - - - - - - - - - - - - - -ccaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - -acataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacctaa