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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatgtagcttcttattatcttgcacatcagttataaactatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG

Basic information

species Arabidopsis thaliana
transcript AT5G55900.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G000280_T01 (Zea mays), 3'ss of exon 1
acaatgtagcttcttattatcttgca----catcagttataaactatcttttgggtct-tttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
   || |   |||  |  |  ||| |    |  ||||| |    | |  ||    | | |||| ||   | ||  |||  |  |    | | |  ||  |  ||||    | |||| || ||||| ||| | |||||  | ||  |||||||||| |||||  |||| |||||||||||||||||||||| 
---atatgctttcgaaaaagattgtaagctcgacagtttttttttctaattcatttttctttacatacatatccaatgcctgctatattctaccgtg--tcacagATCAAATTCACCATCTGTGAAGGAGAAGATGGCACTGAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATACAA

upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G020775_T01 (Zea mays), 3'ss of exon 1
acaatgtagcttcttattatcttgcacatcagttataa---actatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
   |  |   | |  |  |  ||| |  |  | ||  |    ||   |  |   ||||  | || | | ||  |||  |  |    | | |  ||  |  ||||    | | || || ||||| ||| | |||||  | ||  |||||||||| |||||  |||| |||||||||||||||||||| | 
-agaaatgcttccgaaaaaggttgtaagtttggtagtatttgctgattcatctttcttccacatatatatccaatggctgctatgttttaccatg--tcacagATCAAATTGACCATCTGTGAAGGAGAAGATGGCACTGAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA

upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G08380.1 (Glycine max), 3'ss of exon 1
---acaatgtagcttcttattatcttgcacatcagttataaactatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
     |||| || |    ||  | |      ||||| |||   |||    |   |   |||       |   | |  || ||| |  |   ||    |   |||| |   | |||||||||||||| ||||||||  | || ||||||||||| |||||  | || |||||||| ||||||||||| ||
ctactaatgcag-tgaaaatgctgtctggattcagtgatat-ttattcactatatagattaagctaactgtagctaattgttt-tggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG

upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G44450.1 (Glycine max), 3'ss of exon 1
---acaatgtagcttcttattatcttgcacatcagttataaactatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
    ||||| ||  |   | |    |    ||    |   |  |||   ||   |   |||       |   | |  || ||| |  |   ||    |   |||| |   | |||||||||||||| ||||||||  | || ||||||||||| |||||  | || |||||||| ||||||||||| ||
ctaccaatgcag--tgaaaatgctgtttgtatttagtgatatttattcgttatatagattaagctaactgtggctaattgttt-tggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG

upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G44420.1 (Glycine max), 3'ss of exon 2
---acaatgtagcttcttattatcttgcacatcagttataaactatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
    ||||| ||  |   | |    |    ||    |   |  |||   ||   |   |||       |   | |  || ||| |  |   ||    |   |||| |   | |||||||||||||| ||||||||  | || ||||||||||| |||||  | || |||||||| ||||||||||| ||
ctaccaatgcag--tgaaaatgctgtttgtatttagtgatatttattcattatatagattaagctaactgtggctaattgttt-tggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG

upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G47100.1 (Glycine max), 3'ss of exon 1
acaatgtagcttcttattatct-tgcacatcagtta-taaactatcttttgggtcttttagatgtctttctgatgtttt---tttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
      |  |     ||| | | ||   |  ||||| |  | |||||  ||    | |    |    ||    ||| ||    ||||   | |  |   |   |||||    | || ||||||||||| ||||||||  | |||||||| |||||||||||  |||| ||||| || ||| | ||||||||
-----atctccagcaattgtatgtgttaaagagttaattgaatatctggtgaaaatgtcgtttcatcttacattgtgttggacttatgggttctctctttactagACTCGGTTAACGATATGTGAGGGTCATGATGGGACTGAGACATCTAATGGGGATGTGTTGATCTTTCCTGACATGGTTAGATACAG

upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G01640.1 (Glycine max), 3'ss of exon 1
acaatgtagcttcttattatcttgcacatcagtta-taaactatcttttgggtcttttagatgtctttctgatgtttt---tttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
    |  | |   |   | | ||     | ||||| |  | |||||  ||    | ||   |    ||    ||| ||    ||||   | |  |   |   |||||    | || ||||||||||| ||||||||  | |||||||| |||||||||||  |||| ||||| || ||| | ||||||||
----ttcatcaaatgtatgtgttaagagttagttaattgaatatctggtgaaaatgttgcttcgtcttacattgtgttggacttatgagttctctctttactagACTCGGTTAACGATATGTGAGGGTCATGATGGGACTGAGACATCTAATGGGGATGTGTTGATCTTTCCTGACATGGTTAGATACAG

upper sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0015g00750.t01 (Vitis vinifera), 3'ss of exon 1
-----acaatgtagcttcttat-tatcttgcacatcagttataaactatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
       ||| | ||    | |  |  ||     ||  |  |    ||     || |  ||   | | |  || ||  ||||| | || | |    | |     ||||     | ||||||||||| |||||||||||  | |||||||||||||| |||||  | ||||||||||| ||||||||||||||
attcatgaatattgccagatctgcagtttatttttccttcctgttgtagtgactgagggttaatggtatgattttgccgttttct-atttttcttctca-----agACCCGCTTAACAATATGTGAAGGACATGATGGAACTGAGACATCAAATGGAGATGTATTAATATTTCCAGACATGATCAGATACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
                    ttctgat  putative branch site (score: 3)
                         atgtttttttatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaatgtagcttcttattatcttgcacatcagttataaactatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG

- - - - - - - - - - - -gcacatc
- - - - - - - - - - - - - - - - - - aaactat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctg