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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagttttgtgttagaacaaactttgaccactatgtgatgaatatatggagttttttttttttgaagtagtcttttagttatgtggattactacatatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA

Basic information

species Arabidopsis thaliana
transcript AT3G10540.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G097821_T02 (Zea mays), 3'ss of exon 6
gtaagagttttgtgttagaacaaactttgaccactatgtgatgaatatatggagttttttttttttgaagtagtcttt-tagttatgtggattactacatatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
                             |   | | | |||||||  |||            ||  || |   |||| | || || ||    | || ||||   ||           | || | | |  |||     ||||||  |||  |||||||||| | |||||| | || ||||| ||||||||||||||||| ||  |||| ||||| || ||||| ||||| ||| | |||||||| ||||| || 
-----------------------------atttccaagagatgaatgcatg----------ccttcaaactgcactttgtggtgatatgagcaaata-atatagactcgac-------acttatttgtactat-----gaacttcatca--cagAAATGATTTATGGGCATTGGGATGCACACTGTACCAAATGCTTTCTGGCTCTTCGCCATTTAAAGATGCTAGTGAGTGGTTAATTTTCCAGAGAATCATT

upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G34430.1 (Glycine max), 3'ss of exon 6
gtaagagttttgtgttagaacaaactttgaccactatgtgatgaatatatggagttttttttttttgaagtagtcttttagttatgtggattactacatatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
                                            ||  |  |||||| ||  |||     |  | ||| |  ||    | |  ||| |||    |||   |    |  | |||  ||       ||  ||  |||   ||||||||||| || |||||||| ||||||||  | |||||||||||||| ||||||||||| || || || |||||||||||||| ||||| ||||||||||||
-------------------------------------------catgcaccgagtttcttcatttc----ttttgtttca--tac-caggtccctatataataacttttctt---ctgtgttttgtttccccccctcaaatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCAAGTGAATGGCTTATTTTTCAAAGAATTATA

upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 6
gtaagagttttgtgttagaacaaactttgaccactatgtgatgaatatatggagttttttttttttgaagtagtcttttagttatgtggattactacatatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
                                                |  |||||| ||  |||     |  | ||| |  ||    | |  ||| |||    |||   |       ||| | |||      ||    |  |||   ||||||||||| || |||||||| ||||||||  | |||||||||||||| ||||||||||| || || || || ||||||||||| ||||| ||||||||||||
----------------------------------------------gcactgagtttcttcatttc----ttttgtttca--tac-caggtccctatataataacttttcttctgttttttgtttttttgccctcaaatatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA

upper sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 7
gtaagagttttgtgttagaacaaactttgaccactatgtgatgaatatatggagttttttttttttgaagtagtcttttagttatgtggattactacatatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
                                     |  |  || | | | |   | ||  |||  |          | ||| |||     |  |  ||   ||||   | ||  |  | ||   || | ||     |  | || || ||||||| ||||| |||||||| ||||||||| ||||||| |||||||| |||||||| || || || ||||||||||||||||| ||||||||||||||||||
-------------------------------------gaaaaaaaaagaagaaaagtgttggtttcaa----------tggttctgtcag--atcatgtactttctttggtggataacatatttactgttgtt----aacttcatacatacagAAACGATCTTTGGGCACTTGGCTGCACTTTGTACCAGATGCTTTCTGGAACTTCTCCTTTTAAAGATGCAAGTGAATGGCTTATTTTCCAAAGAATTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
    ctcttac  putative branch site (score: 3)
                                          cttattc  putative PPT
           ttagaacaattttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagttttgtgttagaacaaactttgaccactatgtgatgaatatatggagttttttttttttgaagtagtcttttagttatgtggattactacatatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
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