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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttgttcaaccttgagagtgcatacacatggtcctagccgttgtacatccaatgagaattttgtatattttttcagGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT

Basic information

species Arabidopsis thaliana
transcript AT1G15110.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 9
-----------------------gtaggtttgttcaaccttgagagtgcatacacatggtcctagccgtt-gtacatccaatgagaattttgtatattttttcagGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT
                        | |  || ||    |||||   |  |||    | | | |  ||||  || |||         |  || |   | |    |||| |||||||| || || |||||||||||||| || ||||||||||| |||||| | || ||||  || |||||| | || || || || || |  || |
gctatgttctgtatttctagtgcttcgaattatttgttcttgatctt-tatattgttagcctttcccgtgagtgcatatttc----accttttgcttctccatagGTAAAAAGGACGCTAGGCCAGTTCACACCAGCACAGTGGGACAAAGATGAGTGGTACCCTCTGCTTGGCCCTTGGAGATTCATCCAGGTGCTGAGCCTAT

upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 9
-------gtaggtt--tgttcaaccttgagag--tgcatacacat-ggtcctagccgttgtacatccaa---tgagaattttgtatattttt----tcagGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT
         |   |  | |||| ||||  ||   ||  |  |||| |||    | | || |   ||  |   |    |||| | || || ||    | |||| |||||||  ||||| |||||||||||||| || |||||||| ||||||||||| ||   || ||| |||||| | || || || || || |  ||||
gtgcttcagaaactaatcttcagcctttggaacttgatttaacattggtagctgaccttttttttcagagtttatttatttagcattttcttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCACAGTGGGACAAGGACGAGTGGCAACCTACGCTGGGTCCTTGGAGATTCATCCAGGTGCTGAGCCTTT

upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 9
-------------------------gtaggtttg-ttcaaccttgagagtgcatacacatggtcctagccgttgtacatccaatgagaattttgtatattttttcagGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT
                         | |  |||| || ||| || | ||   |    | |  ||  ||   ||||  ||  | | || ||||| |   | |  | |||| |||||||  ||||| |||||||||||||| || |||||||| || |||||||| ||   || ||| |||||| | || || || || || |  || |
cttcagaaactaatcttcagccctcgaatctttgatttaacatttatagctga----ccttttctcagagtttgtttatttatttagcattttct---tctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAGTGGCACCCTACGCGGGGTCCTTGGAGATTCATCCAGGTGCTGAGCCTCT

upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 10
------gtaggtttgttc--aaccttgagagtgcatacacatggtcctagccgttgtacatccaatgagaat----tttg-tatattttttc------agGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT
      ||  |||  |||  |   ||   | |  ||  |     | |||   |   |  ||   |   || |    |||| |||  || |||      |||||||| | ||| | || || ||||||||||| || ||||||||||||||||||||||| ||||  || ||||||||||| |||||||| || | |||||
gactatgttagttgattcttagtgttagtaattaatttattgattgctaagtggactgaatgtgacttgagtgctctttgctatggttcttcgttatcagGTGAAACGAACATTAGGCCAATTCACACCAGCACAGTGGGACAAAGACGAGTGGCATCCACTGCTTGGTCCTTGGCGTTTCATTCAAGTGCTTAGTCTTT

upper sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 10
-------------gtaggtttgttcaaccttgagag--tgcatacacatggtcc-tagccgttgtacatccaatgagaattttgtatatt---ttttcagGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT
              | | | ||   ||  |  |     |||||   ||||     || | | |    || | |    | |    | || |   ||  ||||||||| | ||| | || || || || ||||| || ||||||||||| |||||||||||  |||  || || |||||||| |||||||| |||| |||||
tggcaaatagacccttgatctgcaaaatttcaatgtgttgcattggcatgaagaataacggataatgattctagattactaccatctactggtttcccagGTGAAACGAACATTAGGACAATTTACGCCAGCACAGTGGGACAAAGATGAGTGGCATCCCTTGCTTGGTCCATGGCGTTTCATTCAAGTTCTCAGTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacacatggtcctagccgttgtacatccaatgagaattttgtatattttttcagGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT
                                            tattttttc  CT-rich tract
                             aatgagaattttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttgttcaaccttgagagtgcatacacatggtcctagccgttgtacatccaatgagaattttgtatattttttcagGTGAAAAGGACACTGGGGCAGTTCACACCAGCTCACTGGGACAAAGACGAGTGGCATCCGCTGCAGGGACCTTGGCGTTTTATTCAAGTACTCACTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG