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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT

Basic information

species Arabidopsis thaliana
transcript AT5G18620.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
||| ||  |||     ||    |  |   |     ||  ||  |     |   | |||  ||||| |||| ||    || ||||||| |||||||||||  || | |||||||| |||| |||||| |||||||| || ||||| || || ||||||||||| ||||||||||||||| | ||
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
-gtaagtgcttgtgtactgag--gctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
  ||  |  |||  |  | |   | || | ||   ||   | ||   |  ||||  || || || | |  | || | |  || ||||||| |||||||||||| |  | || ||||| |||| ||||||||||||||| || || || || ||||||||||| || ||||| ||||||||| | ||
gttagttttttgcttcataaaatgttgcttgacaaatgaaaatt---caaacatcaat-taatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttt--------tctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
||| |   |||     ||    |  ||  ||| ||     || | |   |  |  ||   ||||  | |        |||    | |  |||||| |||||||||||  | || ||||||||| | | ||||||||||||||| || |||||||| || |||||||| || |||||||| |||||| | ||
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
gtaagtgcttgtgtactgaggctgttagatgtattgg--attttctcttac-atatatatactgatttcttt--------tctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
||| |    ||     ||    || ||  ||| |     |||||   |||| |  |  |||  ||||  | |        |||||  | |  |||||| |||||||||||  | || ||||||||| | | ||||||||||||||| || |||||||| || |||||||| || |||||||| |||||| | ||
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 13
gtaagtgcttgtgtactgaggctg----ttagatgtattggattttctcttaca---tatatatactgatttct--tttctttgctt-tccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
||||| | || || | |    ||     ||   | | |||    |    |||     ||||||   || |      | | ||||  | | ||||||||||||| |||||||||||||||||||| |||| ||||||||||||||| |||||||| || || || |||||||| ||||||||||||||||||||
gtaagggtttctggattttatcttcgtttttattattttgttgctagatttatggattatataacatggtacacaatctatttgtgtatgcagCTGTTAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
gtaagtgcttg------tgtactgaggctgtta--gatgtattggattttctcttacatatatatactgatttcttttctttgc-tttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
||||| | ||       | ||     | | |||    | | ||| |   |   |    ||||||   || |    | | ||||  | | ||||||| ||||| |||||||||||||||||||| |||| ||||||||||||||| |||||||| || || || |||||||| ||||||||||||||||||||
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 13
gtaagtgct---tgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctt-tccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
||| |   |   ||  || |    ||  |   | |  || |  || | |    | | ||   || || | ||  |||   | | |||| || ||||| |||||||||||||||||||| |||| ||| ||||||||||| || ||||| || ||||| |||||||| |||||||||||||| |||||
gtatggattcaatgaataatttttcttgtttctttgctgaaagttgtgtggattgtctaatgtggttccattgatttttatgtgcagCGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAGGATATTGATAGAAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
gtaagtgcttgtgtactgaggctgttagatg---tattggattttctcttacatatatatactgatttctttt-ctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
||| |   |     | | |   |  | | |    |  || |  || | |    | | ||   || || | ||  ||||  | | |||| || ||||| ||||| |||||||||||||| |||| ||| ||||||||||| || ||||| || ||||| |||||||| ||||| |||||||| |||||
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
gtaagt-gcttgtgtactg-aggctg--ttagatgtattggattttctcttacatatata----tactga---tttcttttctttgc-----tttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
|| ||    || || | |  | |||   || |   |||   ||  |   | | | |  ||     ||| |   ||| || | ||||      ||| ||||||| || || |||||| | || |||||||| || | ||||||||||||||| || || || || |||||||||||||||||||| || || ||||| ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ32950 (Selaginella moellendorffii), 3'ss of exon 12
gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctt--tccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
                              ||||  | ||   | || || |  | | |   ||| |     ||||||    |||||||||| ||||||||| | |||||||||||  |||| || || || ||||| || |||||||||||||| || || || ||||| ||||| ||  | ||
------------------------------gtatgtggttaaatgtttca-acgt-tgccactttttgacacttgcttggcacagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 12
gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctt--tccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
                                             || || |  | | |   ||| |     ||||||    |||||||||| ||||||||| | |||||||||||  |||| || || || ||||| || |||||||||||||| || || || ||||| ||||| ||  | ||
--------------------------------------------gtttca-acgt-tgccactttttgacacttgcttggcacagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtattggattttctcttacatatatatactgatttcttttctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
                            tactgat  putative branch site (score: 2)
                              ctgatttcttttcttt  CT-rich tract
         attttctcttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT