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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA

Basic information

species Arabidopsis thaliana
transcript AT1G62430.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
----tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtg-cagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
    | |||||        ||   | || ||  |   ||   ||  ||   |  |  | ||  | |||  | | |||  | |  | |    |  |||  || ||||| |||||||||||| |     |  | ||||| |||||||||||||||   || |||||||| || ||||| ||||||||||||||||| || || || |
ctgtttttgtttttcgtttgaattttgttttttatcatg---ttttccaagcaat--ggatgtttttggctaaagttaataagttattacatgtattgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA

upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 3'ss of exon 8
---------tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
           || | |  |  |  |||   |     || |   |  |     | |   | |      | |  |||   |  | |      ||   |  |||| ||||| | ||||||   ||| || | ||  | ||| ||||||||||||| |||   || || ||||| |||||||| |||||||| |||||||| ||||||||||
gtaagaaagcattttgatgtttcttataagtgaaccggagttctcattccatgtct---tctagtccttgtgccatccagcctttttgtcatcctttctattt-tgcagATCCCTTGGCGAGAAGTGGCAATTATGCCTATTCAGTGGCATGCCTTAGCTCTTGGCTTGTTTGCTTCAATAATAGCACCATTTGGAGGGTTTTTCGCTA

upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 8
----tcttgt-tagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
    | |  | || |  |     | | || ||  | | |     |||  |||||   ||  | || ||| |    ||||    | |   | |||  ||    ||||| || ||||| ||| |  | ||  | ||||| |||||||||||||||  ||| ||||| || || ||||| |||||||| |||||||||||||| || |
tatatttaatgtaccacatcatcattggttttgcattatctttctagagtttctagatgtttgattttgtactctgttt---gaatacatcgtttcttaa--cagTTCCCATGGAAAGAACTAGCTATTATGCCTGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCATCAATAATAGCACCATTTGGAGGATTTTTTGCGA

upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 8
tcttgttagctaacagatagtagtgtta--gactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
   |||| | |     |   ||   | |  |  | |||| |    ||||    ||     || ||  ||  |   |||      |   ||   | |   ||||| || ||||| ||  |  | ||  | ||||| |||||||||||||||  ||| ||||| || || ||||| |||||||| || ||||||||||| || |
--atgtttgattgtgtactctatcatcattggttttgcgttatctctttagagtttctagatgtttgatttgtactctgtttgattacgtgtctcttaacagTTCCCATGGAAAGATCTAGCCATTATGCCTGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCGTCAATAATAGCACCATTCGGAGGATTTTTTGCGA

upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
-tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
   |    ||  | ||    ||| |  |    ||       ||  |    |   |  | | | | ||| |  |    |    |    |||   || | |||||| ||||||| || ||  | ||||| ||  |||| |||||| ||||||| || || ||||| |||||||| || |||||||||||||| || || || |
cattaaaaagtgaccattctgtattcatgagatgctaatccagattcctggaacgtctgaaaat-cataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA

upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 8
-tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
        ||  | ||    ||| |  |    ||      |||  |    |   |  | | | | ||| |  |    |   ||    | |   || |||||||| ||||||| || ||  | ||||| ||  |||| |||||| ||||||| || || ||||| |||||||| || |||||||||||||| || || || |
aataaaaaagtgaccattctgtattcatgagatgccaatctagattcctggaacgtctgaaaat-cataacttacgacccattatatgctgtcttatgcagTTTTCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTAGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA

upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 9
--tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
  |   | ||     | |||   ||  |  || | |    ||    | ||      || |  | |  |     |  |||    ||||  |||  ||||||||||||||||||||||  |  | ||  | || ||||||||||||||||||||  |||||||||| || ||||| ||||||||||||||||||||||| || |
tgtaaagctattcctctgattaaagcatgggatt-taaattttcaatctcaaaaaaaagatcagta-actctctccctctctcttctcattctcttgtgcagTTTCCTTGGAAGGAGGTCTCCATTTTACCAGTTCAGTGGCATGCTTTATGTGTCGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGATTTTTTGCAA

upper sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 8
--tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
  |   | ||     | |||   ||  | ||| | |    ||    | ||      || |  | |  |     |  |||    ||||  |||  ||||||||||||||||||||||  |  | ||  | || ||||||||||||||||||||  |||||||||| || ||||| ||||||||||||||||||||||| || |
tgtaaagctattcctctgattaaagcatgagatt-taaattttcaatctcaaaaaaaagatcagta-actctctccctctctcttctcattctcttgtgcagTTTCCTTGGAAGGAGGTCTCCATTTTACCAGTTCAGTGGCATGCTTTATGTGTCGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGATTTTTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA
                                          ttcattt  CT-rich tract
     tttgaataatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtgcagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - -aacagat
- - - - - - - - - - - - - - - - - - - - - - - - tgtttga