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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaactgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA

Basic information

species Arabidopsis thaliana
transcript AT1G63700.1
intron # 2
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 2
lower sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 3
ataaactgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccc--tgttttgat-cggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
      |  | |  ||| |||          || | ||   |   || |    | |  | |             |  | ||  |||| |    | |   ||||||| ||||| || |||||||| |||||||| ||||| |||| ||  ||||||||||| |||| ||| |||||| | || |||||||| 
---tcttactgttctctattctgggggaggggattggggccatgtaacttcggtgtccccacaatgatttgtcctcctaatgtggttttaccatttatatcagTGATAGTGGTGAAATGTGTGCGATGAAAGAAGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAAAGTGCAAAGCAGTTGGGGCAG

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 2
ataaactg---atttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgat-cggttatgttttcttcc-tcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
||  |||    |||||  |  ||  ||||  || |  || |    | ||||  ||   ||| |||     |||| | ||||| |  | || | |  | |  | ||||| ||||| || ||||| || |||||||||||||| |||| ||  ||||||||||| |||| |||||||||| | ||||||||||| 
atccactttccatttgagcaattttcaaatcat-gcttaagtttccgcaaacctttgctttgtata----ccctatcttgataccatcatctgtattactattagTGATAGTGGTGAAATGTGCGCAATGAAAGAGGTTACCCTATTCTTGGATGATCCTAAATCAAAGGAGAGTGCAAAGCAATTGGGGCAG

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
---ataaactgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttat-gttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
      ||| |||  |   |||       |   |     | |   | | | ||     |    ||    | ||| |||| || | |||| ||  |||   ||||||| |  || || |||||||| ||||| ||||||||||| | ||||||||||||||| ||||  || |||||| ||||  || | || 
taatctaacggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcat----cgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
ataaa-ctgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttat-gttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
||||  || |  | |  |||      | ||   ||  |    | |  | | |  |  || | |||   || | |||  || | | ||  |  |||   ||||||| || || || |||||||| ||||| |||||||| || | ||||||||||||||| ||||  || |||||| ||||  |  | || 
ataactctaaactatcatctgtcttgactagctaaatgttttattgcact-tggtcattatttgtt-tccttatttgaattgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
ataaactgatttgttctcttcacaaaatattgaatagg-agaactcaaatgttata---tttcta-tgtcacccctgttttgatc--ggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
     |||  ||||| |  || |||  |   |  ||   |  | ||     ||| |   ||| || | | ||  ||| ||||||   | |||  || |  |||  ||||||||||| ||||||||||| ||||| ||||| ||||| |  ||||||||| |||| |||||||| ||||| |||||| | || |||
-----ctg--ttgtttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
ataaactgatttgttctcttcacaaaatattgaatagg-agaactcaaatgttatatttctatgtcacccctgttttgatcggtt-atgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
 |   |||  | |||    || |||  | | |  ||   |  | |      ||| ||   |   ||       | |   |  ||| |  || |  |||  ||||||||||| ||||||||||| ||||| ||||| ||||| |  ||||||||| |||| |||||||| ||||| |||||| | || |||
ttgttctg--tcgtttgtgtctcaaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 1
-ataaactgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
 ||    ||  ||  ||| || |    |       |   |   ||||    |||| | | |||    |     ||||  |    | |   ||   | | ||||||||||||||||||||||| ||||| ||||||||  |||  ||||||||| | ||||||| ||| |||||||| ||  |||| |||
gattgcttgcatttgtctatttaatttaagcaatctgctatttctcatgcattat-tctttataattctgactttttttttttcttttgcttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA

upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 4
-ataaactgatttgttctcttcacaaaatattg--aataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
 |   | || ||   | | |  |   | | |    |||  |  |  ||  |||  ||  |||| | | |   |||  ||  |   || || ||    | | ||||||||||||||||||||||| ||||| ||||||||  |||  ||||||||| | ||||||| ||| |||||||| ||  |||| |||
cagtgattgcttgcatttgtctatttagtttaagcaatctgctatttctcatgc-attattctttat-atatctgactttttttcttttgcttgga-ctttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgttatatttctatgtcacccctgttttgatcggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
                           ttttgat  putative branch site (score: 4)
                                     ttatgttttcttcctc  putative PPT
     ttatatttctatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaactgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - -gatttgt
- - - - - - - - - -tcacaaa
- - - - - - - - - - - - - - - - - - - - -actcaaa