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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcagtgaattctatccattcttctgatacctcgttttccttcatccttcattagttggagaattagatgaacatggattttaattttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT

Basic information

species Arabidopsis thaliana
transcript AT1G63700.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 6
gtgaggcagtgaattctatc--cattcttctgatacctcgttttccttcatcct--tcattagttggagaattagatgaacatggat----tttaattttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
|| |         | || |   | ||  |     || ||  || | |  ||       |  |  | |   ||||  | |  ||   |    ||  ||  | | ||||||||| ||||| ||||| ||| |||| |||||| |||| || |||||  ||||||| || || ||||||||||||
gtaacattccatttccttttgtcgttagttcagcacttcagttccttagatgtaagctaccaagttgtagattattttattatttgtcatgttccataatttgcagGGACATTAAAGGTGCAAACATACTGGTAGATCCTAATGGTCGTGTAAAGCTTGCTGACTTCGGAATGGCAAAACAT

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 6
gtgaggcagtgaattct-atccattcttctgatacctcgttttccttcatcct-----tcattagttggagaattagatgaacatggattttaattttatt--cagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
|| |   | |   ||   || |  | ||| | |   |  ||||  | ||| ||     |      ||  |   ||   |   | |    | |   |  |||  ||| ||||||||||| ||||| |||||||| || ||| |||| || |||||  ||||||| ||||||||||||||||||
gtaacataatttttttagattcccttttccggtctattatttta-tgcatactaggggtttgctattttatcttttcttttgcttactctcttcctaaatttgcagAGACATCAAAGGTGCAAACATATTGGTAGACCCTAATGGCCGTGTAAAGCTTGCTGACTTTGGGATGGCAAAACAT

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 5
gtgaggcagtgaattctatccattcttctgatacctcgttttccttcatccttcattagttggagaattagatgaacatggatttta---attttattc----------agGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
|| |   | |   |    |   ||| | |   | |   || |  |         |   ||  |  | ||  ||     |   |||||   | | | |||          || ||||||||||| ||||| |||||||| || ||| |||| || || ||  | ||||| ||||||||||||||||||
gtaacataatttgtatagtt--ttccttttccagcctattattttatgcttactagaggtctgctatttttatttttttttcttttacttactctcttcctaaatttgcagAGACATCAAAGGCGCAAACATATTGGTAGACCCTAATGGCCGCGTGAAGCTCGCTGACTTTGGGATGGCAAAACAT

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 5
-gtgaggcagtgaattctatccattcttctgatacctcgttttccttcatccttcattagttggagaat-tagatgaacatggatttta-attttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
  |||     || | | | |  |   || ||  |     |      |  |   | ||| ||   | ||| |     |   ||     || ||| |  |||||||||| ||||||||||| ||||||||||| |||  ||| ||  ||||| | || ||||||||||||||||| |||
catgaatttctgtaattttttaaagtttatg-catagtataaattatagtttgtgatttgtgaaacaatctctcctagtctgatcactacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 5
---------gtgaggcagtgaattctatccattcttctgatacctcgttttccttcatc--cttcattagttggagaattagatgaacatggatttta------------attttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
         ||    || |  |  | |        |||   |  ||  ||||  | |||  ||| | || |       ||| |   |  |   | ||             |||||| |||| ||||| |||| |||||| ||||||||||||||| ||||  | |||||| | || |||||||| |||||||| |||
gtgagtcttgttgatcattataacccacatgactatcttcaagttctgtttcaattatcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 8
gtgaggc--agtga--attctatccattcttctgatacctcgttttccttcatc------cttcattagttggagaattagatgaacatggatttta------------attttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
||||| |    |||  ||| || |||     ||     |  ||| |  ||||        ||| | || |       ||| |   |  |   | ||             |||||| |||| ||||| ||||  ||||| ||||||||||||||| ||||  | |||||| | || |||||||| |||||||| |||
gtgagtcttgttgatcattataaccacatgcctatcttcaagttctgtttcaatcatcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCCGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------gtgaggcagtgaatt-ctatccattcttctgatacctcgttttccttcatccttcattagttggagaattagatgaacatggattttaattttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT------------------------
                                       ||||  | | |   ||  ||  |       | ||| | |   ||  || |     |      |   ||  |    |  | |||  ||  | || |||||||||||||||||||||||| ||||||||||  |||| |  || ||| | || |||||||| |||||||| |||                        
gtaagtcagatcaccttacattgttggtttggttatcctaggctatcattcattactcacccccaatgaatctcatctgttttagtcatcttagaacatctgtgctaattaggta-agttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCATGTGAAATTGGCAGATTTTGGAATGGCAAAGCATGTAAGAGTATTCACATGCATTTTT

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------gtgaggcagtgaattct-atccattcttctgatacctcgttttccttcatccttcattagttggagaattagatgaacatggattttaattttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
                                       ||||  | | |  | |  ||  |       | ||| | |   ||  || |     |      |   ||  |    |  | |||  ||  | || |||||||||||||||||||||||| ||||||||||  |||| || || ||| | || |||||||| |||||||| |||
gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggta-agttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatccttcattagttggagaattagatgaacatggattttaattttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
                                       ttttaat  putative branch site (score: 3)
                                             ttttattc  CT-rich tract
                               aacatggattttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcagtgaattctatccattcttctgatacctcgttttccttcatccttcattagttggagaattagatgaacatggattttaattttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT