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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G65410.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g46740.2 (Oryza sativa), 3'ss of exon 8
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
                  ||   | |  ||| | ||   || |||   | |  | | ||| |   ||  |       | || |   ||   | | |  |   |   | |      |   |  |     |   | || || |  ||||  |||||||||||||||| |||||||||||||| || |||||||| || || |||||||| |||||||| || || ||  | ||||   |||||||  
---------------gtataccctgactaatctcttcagtcattacgag-taaattgctgtaatagttcacaggaaaaggagatcaaacagcttaacttactattgactgtcttcttgatattatacattttttccattac--agGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 8
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
          |||  |         | ||| | ||||     ||      || | |   | ||   |||| |      ||||    |||| |    | || | | ||  ||    ||  |||    | |      | | |  ||||| ||||| || ||||| || || ||||| || || || |||||||||||||| || ||||| |||||||| ||||| || ||||| |     |||||  
---------gtattgatgatgagctaagaaggcgttttcctctt------tttattatcggat--atatactc-----tgaactggaaaggctgtttctgtccataagcagacgctc-cttacatttctt-----cctctggtagGTCCTTTTATATGATGAACCTACAGCTGGGCTCGACCCGATTGCATCAACTGTCGTGGAAGACCTTATACGTTCTGTGCATATGACTGGACGGGATGCCC

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 7
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
                                         ||| ||    | |       |  | ||  |||||| |    |   |||  |  |   |  |     |  |    | |  ||    |||   | | | |   |||||||| ||||| || || |||||||||||||||||||| |||||||| ||||| ||||||||||| || || ||||| ||||| | ||   |||||||| 
---------------------------------------ctttttgaaatctcatgatataacttttactgttattca----atcaaaaccctccccttatctcttttctgtttataaaataaacattttg-tacttctgtataGGTGCTCTTGTATGACGAACCAACTGCTGGACTTGATCCCATTGCATCTACTGTTGTTGAAGATCTGATTCGCTCTGTGCACATAAAAGGACAAGATGCA-

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 7
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatc-tgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
                                              |  ||    |  |  | | | ||   |||||     ||| |  |  || |   |        |  |    | |   | |  |||  |  | | |    ||||||| ||||| || || |||||||||||||||||||| |||||||| ||||| ||||||||||| || || ||||| ||||| | ||    ||||||| 
---------------------------------------------aaatctcatatgatataacatttacttttattcgatcaacatgtacccacctcttctgtcttttctgtttataaaacaagcattttgc-acttctgtacagGTGCTCTTGTATGACGAACCAACTGCTGGACTTGATCCCATTGCATCTACTGTTGTTGAAGATCTGATTCGCTCTGTGCACATAAAAGGACGAGATGCAC

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 7
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
                                       | || |||      | |    ||    || |     | | ||     |   |  |  ||| ||     ||  |   | |||| ||| |||||||     |   |||||||| || || ||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| || || ||||| ||  | | ||| ||||||||| 
--------------------------------------gtgttaagaaatacaatttaatcaaagttagaccatgttacgagcgccagtcttgtt-tgtagcg---tttttgttctaatttttggttttcact---cctgaatagGTGCTATTATATGATGAACCAACTGCTGGGCTTGATCCAATCGCATCTACTGTAGTTGAAGATCTCATCCGCTCTGTCCATTTAAAAGAGGAAGATGCAC

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ22908 (Selaginella moellendorffii), 3'ss of exon 6
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
                                                                                         || |   | | || |  || |       |||  | | |   | | |   |||  ||||  |  |||| || || |||||||||||||| ||||| ||||| || ||||| || || |||||||| ||||| || ||||| | ||     |||||| 
-----------------------------------------------------------------------------------------gttagttttttgctagcatga------tattcgtagatcagaattctccttcacagGTTGTCATGTATGACGAACCAACTGCTGGACTCGATCCCATTGCTTCGACTGTTGTCGAGGATCTTATTCGGTCAGTACACATCAAAGGGCGTGATGCAA

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ30431 (Selaginella moellendorffii), 3'ss of exon 6
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
                                                                                         || ||  | |  | |  || |       |||  | | |   | | |   |||  ||||  |  |||| || || |||||||||||||||||||| ||||| || ||||| || || |||||||| ||||| || ||||| | ||     |||||| 
-----------------------------------------------------------------------------------------gttatttttttcctagcatga------tattcgtagatcagaattctccttcacagGTTGTCATGTATGACGAACCAACTGCTGGACTTGATCCCATTGCTTCGACTGTTGTCGAGGATCTTATTCGGTCAGTACACATCAAAGGGCGTGATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG
                                    tttcactgccttttct  CT-rich tract
            aaaaattaggaattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG