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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacacaagcgttttttgctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag

Basic information

species Arabidopsis thaliana
transcript AT4G22360.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g39310.1 (Oryza sativa), 5'ss of exon 3
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacacaagc--gttttttgctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag
||  |||||| | ||||| | || |||||||| ||| ||||||| |||||||||||||| ||| |  | ||||||||||||   || |||||  ||  |||||    ||   |||   |  | | | | |||      ||    ||||   |||||   ||  | | | || |  |    |||   |   
TGCAATGATGAGCTGCGTCTAGTCTTTGAGACAGATAGCACTGATATGTTCAAGATGAACAAGCTTTTAGCTAAGCATATTAGACCACTTGAGGCAAAAAgtaggtcttcttcactctccagctatgttctgcaaaataatcaagctt---ttgtttgtgg--aataagtgctcaaaattcttgcag---

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G332809_T01 (Zea mays), 5'ss of exon 9
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacacaagcgttttttgctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcac-ttttggcag
||  |||||| | | ||  | ||||||||||||||| |||| ||||||||| ||||||||||| | ||  | |||||||| |  || || ||      |||||   |||   |   |       |  ||  |||           |  | | |||    |||||||   | ||   ||  || |  |||
TGCAATGATGAGCTCCGATTAGTTTTTGAGACTGATAGCACGGACATGTTCCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgtttctcctgatgcacaatatctttgttttgcagaaaaatactatcttct---ttactgaacatgtggtccaaattgtaccag

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G035325_T01 (Zea mays), 5'ss of exon 3
---TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCAT---CAAgtaatggttaaacacaagcgttttttgctgagttc-caactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag--------
   ||  |||| |   | |||||||||||||| |||||   ||| |||||||| || |||||||||||| | |||||||| ||   ||| ||||| |||    || |      ||      || |    |   ||   ||  |   || | |      ||| |    |      || |  |||   |  |             
ATTTGCAATGACGAACTTCGTGTGGTTTTTGAAACTGACACCACCGACATGTTTAAAATGAATAAGTTGTTGGCTAAGCACATAACCCCACTTGACCCAAgtacatgcttctatttcttttaatcagcatacactaccttttcttttgcgttactaaagtttagtcctggaatatgctcaagtgcttcctaatgacaccgcag

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G43590.2 (Glycine max), 5'ss of exon 3
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacacaagcgttttttgctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag
||  ||||||   |||||||||| |||||||| ||||| ||||| |||||||||||||||||||||||  ||||||| ||| |||| ||||| ||| | ||||    |  |    | || | ||||  |||  |     | |  |||  ||||| ||  |  ||   | |||| | ||||||  |   
TGCAATGATGAACTGCGTGTGGTGTTTGAGACGGATTGTACTGATATGTTCAAGATGAATAAGTTGCTATCTAAGCACATTATCCCCCTTGAACCAACCAgtaggtatctaggttatgcttatttttatgacattgtggttta-ttgtgttgtttaaatt--cttcttttttgtg-cactttcag---

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G39530.1 (Glycine max), 5'ss of exon 3
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacacaagcgttttttgctgagttccaactgt-gcttggtttgttcaaggttactgactgtttgagtcacttttggcag------------
|||||||||||  ||||| |||| |||||||| || ||||| |||||||||||||||||| ||||||| ||||| || ||| |||| ||||  ||  |||||||    |||| ||     |  | || |  | |  |  | |   |  || | |  | |   |   | |      || |  |     |             
TGTGATGATGCACTGCGTTTGGTATTTGAGACAGACTGCACCGACATGTTCAAGATGAATCAGTTGCTAGCTAAACACATTATCCCACTTGGACCTACAAgtaagtagtaaataccca-atgctctgtttggataaacttctcaataagtatttataggaaaataaaataagaaggtaaaataaattaagattctcccata

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G01230.1 (Glycine max), 5'ss of exon 3
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacac---aagcgttttttg--ctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag-------
|||||||||||  ||||| |||| |||||||| || ||||| || ||||||||||||||| ||||||| ||||| || ||| |||| |||| |||  |||||||    |||| ||   | ||  | ||||   | | |||    |  |  |   | |   |||   |      | |  | | | ||  |           
TGTGATGATGCCCTGCGTTTGGTATTTGAGACAGACTGCACCGATATGTTCAAGATGAATCAGTTGCTAGCTAAACACATTATCCCACTTGGTCCTACAAgtaagtagtaaatacccaatgctctgtttggattaacttctcgataagtatttataggaaaagaaaataagaaggtaaaataaattaagattctcccata

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0187g00190.t01 (Vitis vinifera), 5'ss of exon 3
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgta-----atggttaaacacaagcgttttttgctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag
|||||||||||  | ||  |||| |||||||| ||||  ||||| ||||||||||||||||||||||||||||| |||||  | |||||||| || |||||||     ||||||| | |||   |   |  | |  || | ||   |      |||| | |||  |  ||  ||||   ||   | || ||||
TGTGATGATGCCCTCCGCTTGGTGTTTGAGACAGATTCTACTGATATGTTCAAGATGAATAAGTTGCTTGCTAAACATATCATTCCGCTTGAACCTTCAAgtatgttaatggttaca-acatatgacatg-gtttggtcctaagaataaagactttgattaagacttttgtttgtt---gtttttgtttgcag

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0187g00240.t01 (Vitis vinifera), 5'ss of exon 3
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgta-----atggttaaacacaagcgttttttgctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag
|||||||||||  | ||  |||| || ||||| ||||  ||||| ||||||||||||||||||||||||||||| |||||  | |||||||| || |||||||     ||||||| | |||   |   |  | |  || | ||   |      |||| | |||  |  ||  ||||   ||   | || ||||
TGTGATGATGCCCTCCGCTTGGTGTTCGAGACAGATTCTACTGATATGTTCAAGATGAATAAGTTGCTTGCTAAACATATCATTCCGCTTGAACCTTCAAgtatgttaatggttaca-acatatgacatg-gtttggtcctaagaataaagactttgattaagacttttgtttgtt---gtttttgtttgcag

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0090g01460.t01 (Vitis vinifera), 5'ss of exon 3
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacacaagcgttttttgctgagttccaactgtgcttggtttgttcaaggttactg--actgt----------ttgagtcacttttggcag-----------------------------
||  | |||| | | ||| |||| |||||||| ||  | ||||||||||||||||||||||||||||| ||||| |||||  |||| ||||| ||  | ||||   ||     | || | |||    |  |    ||  ||  | |   |     || |||| |   ||  |          || | |||||  |                                  
TGCAACGATGAGCTACGTTTGGTATTTGAGACAGACAGTACTGACATGTTCAAGATGAATAAGTTGCTAGCTAAACATATAATCCCTCTTGAACCTACTAgtatgtgtc---tataatcttttcacacaaacacgcacatgatcgtatatcaaaaaatgttaatacaacaataaaataaaaattaaatcactcatatggattaagcttttcttgttttgatccttgcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|47830511|gb|CK120195.1|CK120195
EST:     CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAA                         AGGACTCTGGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGACTAAGACTG
genomic: CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggtta ... cttttggcagAGGACTCTGGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGACTAAGACTG
EST: gi|47828877|gb|CK118561.1|CK118561
EST:     CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAA                         AGGACTCTGGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGACTAAGACTG
genomic: CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggtta ... cttttggcagAGGACTCTGGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGACTAAGACTG
EST: gi|47830960|gb|CK120644.1|CK120644
EST:     CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAA                         AGGACTCTGGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGACTAAGACTG
genomic: CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggtta ... cttttggcagAGGACTCTGGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGACTAAGACTG
EST: gi|124723805|gb|EH815207.1|EH815207
EST:     CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAA                         AGGACTCTAGGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGA
genomic: CAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggtta ... cttttggcagAGGACTCT-GGTCAAGCAAAAAAGGCAAAAACTGAGGTGGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGATGATGCGTTGCGTGTGGTTTTTGAGACTGATTGCACTGACATGTTCAAGATGAATAAGTTGCTTGCTAAGCATATTCTCCCGCTTGATCCATCAAgtaatggttaaacacaagcgttttttgctgagttccaactgtgcttggtttgttcaaggttactgactgtttgagtcacttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG