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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG

Basic information

species Arabidopsis thaliana
transcript AT1G09100.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
---gtatgaaaactagagtaaacgt-aactgattttgatcttgttcctgtgatattttttga-accaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
   | ||      | |    |  ||      |||||  || | |    ||  |  |  |||   | | |   | | |||  | | |  || ||  ||  ||||||||||||| ||||| ||||| |||||||||||||| || | ||||||||| ||||||||||| || || || || || ||||| ||||||||||| |
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttctgcttgctgctagatacatattaatgtctatgcgaattg-gtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 5
--gtatgaaaa--ctagagtaaacgtaactgatt-ttgatcttgttcctgtg-atattttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
   |||||| |  || |  |  |     ||  || || |   | | | ||   ||  ||||  | |  |||   ||  |  ||||||| | |||  |   ||||||| ||||| ||||||||||| || || || |||||||| | |||||| || |||||| | || || || || ||||| ||||||||||| || || |
acatatgaacagccttgccttcagaagtctatttatttactatttacttgcatatggttttctagcgcaacaataatcatatttttttgggctt--gcccagATGTTTATCGGTGATGGAGCAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G173849_T01 (Zea mays), 3'ss of exon 1
-----gtatgaaaac-tagagtaaacgtaactgat---tttgatcttgttcctgtgatattttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
       ||| | |  | |  | | | |     ||   ||| ||  ||  | |    ||| |||||||  |   ||  ||||||  | ||    ||   ||  ||||||| || || ||||||||||| |||||||| ||||| |||| |||||| ||||||||| | |||||||||||||| || |||||||| || || || |
cgacaaaatggagatattgcattaccatggaaaatctgttttattctgagcatactttatattttgaagta---gggtagtaacgatgttcttgctg--gttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
----gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaac-caaacg-gaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
     |   |  || |  | |||  |   | ||| |||| || |       | | ||| |     |||    || ||||||  | ||    ||   ||  ||||||| || || ||||||||||| |||||||| ||||| |||| |||||| ||||||||| | |||||||||||||| || |||||||| || || || |
agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagtatgatagtaacgatgttcttgctg--gttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 5
--gtatgaaaactagagtaaacgtaactgat---tttgatcttgttcctgtgatattttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
   |     |  |    |  ||   |||      |||| |  | |||  ||  | ||   ||          | | | |  |    |  | || |||| |||||||||| |||||||||||||||||||| |||||||| || |  || ||||||||||| || || || ||||| || |||||||| ||||| ||||| |
gtttcctctatttcacttgcacactactaccttatttgtttgtattcacgtc-tcttgactgggtttggattataatgatctaacctgcaattttgtacagATGTTCATAGGAGATGGAGCAAAACTTGTTCGTGATGCCTTTCAACTAGCAAAAGAGAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
----gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaacca-aacggaa-agtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
     ||  |    |  | |     ||  || ||     | |||   |||| |   |    |     || |||  | |||  |    |  | || |  | ||||||| || ||||| ||||||||||||||||  ||||| || | ||| ||||||||||| || || || |||||||| |||||||| ||||| ||||| |
atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaatttt--acagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
--gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatatttt--ttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
   |     |  |    |  ||   | ||  |||  | ||  |  |   |  | ||   ||          | | | |  |    |  | || |||| |||||||||| |||||||||||||||||||| ||||| || || |  || |||||||| || || || || ||||| || |||||||| ||||| ||||| |
gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaaccaaacggaaagtaactttttttagact------------tatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
  || ||   |          ||| |   ||     || |     ||| | |  |||| |   | ||  | ||  | || ||| | |            || | ||| |  |        | |  ||||||||||||||| ||||| || | ||| ||||||||||| || || || |||||||| || ||||| ||||| ||     
--atcaatctttttcagctaataattttcttgtgatttttgttgatgaaactcattga-ctgtatggggattagttattcttatattatgtcttcatattaagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
----gtatgaaaactagagtaaacgtaactgattttgatct-tgt-tcctgtgatat-tttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
     | |     | |      |  ||  | | | |||| | ||  | || |||| | || ||  |  ||| | ||   |||   ||   |   | | |  |||||||||| || ||||| || ||||||||||||||||| || | |||||| ||||||||||| ||||| || || || |||||||| ||||| || ||||
aattctctagttgccatgtagcaattatgttagtgtgatgtgtgcattctttgatctattcttttattaaatgtaaccaaacaactt---ggaatgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
                    ||      |    |   | | |||||    || ||  |  ||| |              ||  |  |  |    ||||||||||||||||||||||||| || ||  | ||||| || | ||| |||||||||||  | || || || || ||||| |||||  | ||||| || |
--------------------gttctgtgtaggaactctttacctgtcgggttcttaaactcaagc--------------ttctggttcgt-cgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
gtatgaaaactagagtaaacgtaactgattttgatcttgttcc-tgtgatattttttgaaccaaacggaaagtaacttt---ttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
                                      ||||  |||   |  | || | |     ||    |||  |     ||     |  | |  ||||||||||||||||||||||||| || ||  | ||||| || | ||| |||||||||||  | || || || || ||||| |||||  | ||||| || |
--------------------------------------gttctgtgtaggaactctttacctgtcgggttgttaaactcaagcttcttgttcgt-tgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

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|164193317|gb|ES024452.1|ES024452
EST:     CACAGACAAATGCAACTTTCCTCAAACTAGCAGGGCCACAACTTGTTCAG                         ATGTTCATCGGAGATGGAGCAAAACTTGTCCGTG
genomic: CACAGACAAATGCAACTTTCCTCAAACTAGCAGGGCCACAACTTGTTCAGgtatgaaaac ... ttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtgatattttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG
                           aagtaac  putative branch site (score: 2)
                          aaagtaacttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatattttttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA