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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatctaagtcaattacaaagctgcacactttgggccgagacataatcagacaaaaatgtttttcctctcttatcgttttgatggtctcttgatagGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG

Basic information

species Arabidopsis thaliana
transcript AT4G34890.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 6
--------------gtacatctaagtcaattaca-aagctgcacact--ttgggccgagaca---taatcagacaaaaatgtttttcctctcttat----cgttttgatggtctcttgatagGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG
               |  || ||   |   | ||  |  |  |||||  |||  |          || |   |   | | ||| | ||  |   ||     | |  |||    |||   |||||||||||||| |||||||| || || ||||| || || ||| ||||||| ||||||||||| || |||||| | || || |  |   ||||||||||  
gtgaggtccgacacatggatgtaccccttctgcatgatttttacactagttgtactttttttcattacttttatttataagttgtgccaatacaatgaggtgatgggattccatctgtttagGTTCCTAATGCATCACCAACAGCAGCCTCTGCTAGTTCAGATCTGTATGGAGCTGCAGTTTTGGATGCTTGTCAACAAATCAAGGTTCGAATGGAACCCA

upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 10
gtacatctaagtcaattacaaagctgcacactttgggccgagacataatcagacaaaaatgttt-ttcctctcttatcgttttgatggtctcttgat-agGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG
     |   | |    | | | |   |     |||      |  |  ||        | | |   || || |  |||| |  || | |   |   || ||||||||||||| ||| |||| || |||||||| || |||||||||||||| || || ||||| || || |||||||| || || ||| | ||||||||| 
tccttttctattttcctcccatgtaccctttcttgaatatggggactattgttttttattctaaattgctgtgatatcctcatggttgctgcaaaattagGTTCCTAATGCTTCAGCAACAGCAGCTTCTGCAAGTTCTGATATGTATGGAGCAGCGGTTTTGGATGCATGTGAGCAAATAATGGCACGCATGGAACCTA

upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 11
-gtacatctaagtcaattacaaagctgcacactttgggccgagacataatcagacaaaaatgtttttcctctcttatcgttttgatggtctcttgat-agGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG
  |   | |   |      |  |  | |     |||   |  |  ||| |    |  | |     || || | || || |  || | |       || ||||||||||||| || ||||| || |||||||| || |||||||||||||| || || ||||| || || |||||||| || || | | | ||||||||| 
tatcattttctattttccccccatttacctttcttgaatctggggatattgtttctgatactaaatttctgtgttgtcctcatgcttgctggcaaattagGTTCCTAATGCTTCTCCAACAGCAGCTTCTGCAAGTTCTGATATGTATGGAGCAGCGGTTTTGGATGCATGTGAGCAAATAATGGAACGCATGGAACCTA

upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 10
--gtacatctaagtcaattacaaagctgcacactttgggccgagacataatcagacaaaaatgtttttcctctcttatcgttttgatggtctcttgatagGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG
   ||    | | |  | ||      ||   | | |      |   |    | ||||   ||  |  |  |  ||| |  || || || |        ||||||||||| |  ||||||| || |||||||| || |||||||||||||| |||||||||||||| ||||| ||||| || | |||| | ||||| ||  
gattattcattattttactatccttttgtggattattaatgaacctagttgccgacactgattctcgtatttacttgtacttgtgttgctgctaaatcagGTTCCTAATTCAACACCAACAGCAGCTTCTGCAAGTTCTGATATGTATGGAGCTGCAGTTTTAGATGCTTGCGAGCAAATAAAAGCACGGATGGAGCCGA

upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ27160 (Selaginella moellendorffii), 3'ss of exon 10
gtacatctaagtcaattacaaagctgcacactttgggccgagacataatcagacaaaaatgtttttcctctctta--tcgttttgatggtctcttga----tagGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG
                                                       |   || |||||  || | |  |  |  | |     |||||     ||||| || ||||| || || ||||| ||||||||||||||||||||||||||||| || ||| | || || ||  | || || | || ||| |||  |||  
-----------------------------------------------------gtacgctgcttttcacctttcaagttctgctcaccacgtcttggaatgtagGTACCAAATGCTTCGCCTACTGCGGCTTCTGCGAGCTCTGATATGTATGGTGCCGCTGTTATCGATGCATGCAACCAAATCAAAGAAAGGATGAGACCAT

upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ33495 (Selaginella moellendorffii), 3'ss of exon 10
gtacatctaagtcaattacaaagctgcacactttgggccgagacataatcagacaaaaatgtttttcctctctta--tcgttttgatggtctcttgata-----gGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG
                                                       |   || |||||  || | |  |  |  | |     |||||  |     ||| || ||||| || || ||||| ||||||||||||||||||||||||||||| || ||| | || || ||  | || || | || ||| |||  |||  
-----------------------------------------------------gtacgctgcttttcacctttcaagttctgctcaccacgtcttggaatgtaagGTACCAAATGCTTCGCCTACTGCGGCTTCTGCGAGCTCTGATATGTATGGTGCCGCTGTTATCGATGCATGCAACCAAATCAAAGAAAGGATGAGACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataatcagacaaaaatgtttttcctctcttatcgttttgatggtctcttgatagGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG
                                   ttttgat  putative branch site (score: 4)
                                            tctctt  putative PPT
         acaaaaatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatctaagtcaattacaaagctgcacactttgggccgagacataatcagacaaaaatgtttttcctctcttatcgttttgatggtctcttgatagGTTCCTAATGCGTCACCAACTGCTGCTTCTGCGAGCTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA