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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaattttaggatcttttccaatgcttttagcttcctggactagttaattttcttagattttcctttcttcagagtgttatttttcaatgtccattctaattcacattgcagGATGTACAAGGATGGTAGCATCATTCCATTAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G60100.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 11
gttaaattttaggatcttttccaatgcttttagcttcctggactagttaattttcttagattttcctttcttcagagtgttatttttcaatgtc-cattctaattcacattgcagGATGTACAAGGATGGTAGCATCATTCCATTAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAG
||    |||||  |  |  | ||     ||||  |      || ||  ||| |    | ||||||   |      | |   | |    |||| |   ||||  ||| |  || ||||| | |||||  || |  |  ||  ||   ||| || |  |||||||||  |||||||||||||||||||| || ||||||  |||  | |||   |||
gtagctttttatcaattcattcaccatctttactt------accaggcaatctgtaaaaattttcaactgc----aatagcaat----aatgccgttttctggttctc--tgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG

upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 11
-------------------------------------------------------gttaaattttaggatcttttccaatgcttttagcttcctggacta-gttaattttcttagattttc------ctttcttcagagtgttatttttcaatgtccattctaattcacattgcagGATGTACAAGGATGGTAGCATCATTCCATTAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAG
                                                         || || |    || | |    ||   | |    |  ||    | |  | |  ||  |  | ||        ||| |  |   |  ||  |||  ||   | |  |||   |  ||  ||||  ||||||||||| |  ||||| || || |||||||||||||||||||||||||| | | | |||||| | || ||||||  |||  | |||   |||
gtatgtaaagcatatcatcctaatcaatattacacatttaataagcaatgggatatatatatatatatatatatatatatatatatcatatattgtgtgatgacagtgatcaaaagtgtttgacagattttttctatcttcgtacatttgtattgacttgttaacctattttaaagGAAATACAAGGATGGAAAAATCATACCGTTGGATGATTCTTTGGATTATGGTGCAAACTATGCTCACATGTTAGGGTTTGATGATCCGGAAATGCTGGAG

upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 11
gttaaattttaggatcttttccaatgcttttagcttcctggactagttaattttcttagattttcctttctt--cagagtgttatttttcaatg---tccattctaattcacatt-gcagGATGTACAAGGATGGTAGCATCATTCCATTAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAG
                  || || ||| |     | | |||| | ||   |  | | | ||  |  |||| |  || ||| |    |     |      |||  |  |   | || | ||| | |||||  ||||    || || ||    ||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||  | ||| |||||
------------------tttcagtgcctc--attacatggaattgtgcttagtatgaaatcatagtttccttacatagtatggaatcatggttggcctcatctttctgtgcttttgaagGGTATACAAAAATGGACAAATTATACCCAAGGATGACTCTTTGGATTATGGTGCAAATTTTTCACACATGTTGGGATTTGATAGTCCAAAAATGCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttcctttcttcagagtgttatttttcaatgtccattctaattcacattgcagGATGTACAAGGATGGTAGCATCATTCCATTAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAG
                                     ttctaat  putative branch site (score: 2)
                  tgttatttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaattttaggatcttttccaatgcttttagcttcctggactagttaattttcttagattttcctttcttcagagtgttatttttcaatgtccattctaattcacattgcagGATGTACAAGGATGGTAGCATCATTCCATTAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG