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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G08040.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 9
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
  | |       |    |     |  |      |     ||  | |  |        |  |  ||  | | | ||    ||    |  | |  ||| ||||| |||||||| ||||||||| |||| || ||||| || |||||||| |||||||||||||||||||||
acatgaaggaaaaacagcaacggcataacaaaacggaaggaggatcagatgttttctttttcttaaaactatccgtcttca--cattctgtttcacatgcagATTTGTTGAAATTATGGCAACTGTGTTCTCTAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 10
--------gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgct-tata-tcaattttcgataacaggtgtgttttcccact-tgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
         ||   |||||| ||   |||     |   |   ||      |      |   | |||||| |  | |  | ||  | ||||   | | | || |   | | ||| |||||||| || ||||| || || || |||||||| |||||| |||||||||||||||||||||||
gtatgtgattatttctctgtcctgagttttgtctacagtacatcccaatatgtatggcgtgaaagtgctatccacttgagttaggctaactaatctatattgctgttgttcagCTTTGTTGAAATAATGGCTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 10
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
                    | | |   |  ||| || |   |      |||| |  ||   | |     |  | ||      |||||||    |  | ||| |||||||| || ||||| || || || || ||||| |||||| |||||||||||||||||||||||
-------------------gtatgtagcttcctc-ctctacttgggtagctgatgtatgtgaagaggggctaactatt-----tgtgtttg---atgtacagCTTTGTTGAAATAATGGCCCCGGTGTTCTCCAGAGATGCATGGAGATGTGTATGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 10
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
||| ||  ||     | |    | | ||| | | | |                | | | |||    ||| | ||  ||  |  |    |||   |  ||||| |||||||| || |||||| | || || ||||| || |||||||| ||||| |||||||||||||||
gtaaggggctaagggcccagaattttattgtgtattt----------------aaatttctttgcccaaatatctgtattacattcaatttg--atgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM5G801369_T03 (Zea mays), 3'ss of exon 10
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatc-aattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
                                     |  | | |  || |  |   |  |  |||| || ||||  |        |||  ||  |  |||||||||||||| ||||||||| ||||||| || || || |||||||| |||||||||||||||||||||
------------------------------gtaggagtgcaatcatttattagattattttcttatcgaaatttctgtttttcacatgtaatctgatatgcagGTTTGTTGAAATTATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 10
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
                       |  ||  |   | | |   |||  | |     | ||  || || | | |||  ||| || |   ||||   |  ||||| |||||||| ||||||||| | || || |||||| | |||||||| |||||||||||||||||||||
----------------gtagggccaaatgtttgttgtgtatttaattttc-----attgtcta-attattattc--taaaagttcaattttg--atgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 10
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatc-aattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
     | | | | |  ||| |    |   |||    ||   ||     |||      | ||| | |  |||| ||  |   |    |   ||   |  ||||| |||||||||||||||||| | || || || ||| | |||||||| |||||||||||||||||||||
---tcgatttatcccttctgtagaccccactcatgtttgacctccaacactaggtcttccttttttttaattatcattctaaaagttcgattttgatgtgcagATTTGTTGAGATTATGGCAACAGTGTTCTCCAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 10
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgata---acagg-------tgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
       | |||  | | |||  ||| | |     |  | || |     |   | | | ||   |||| | | | |||   ||||        | ||| | | |  || ||| |||||||| || ||||| || || || || ||||| |||||| ||||||| |||||||||||||||
------gtatgtgtttttttttcctcctcccagaacacttaccagttccc---ataatactaccatcagtctcccatacatacagaggcaacttatgtatgctctattacagTTTTGTTGAAATAATGGCTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 10
----gtacggctctgtactctctttc----tctcattc-tctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgc------agGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
    |  |     |  || ||  |||    |   |||  | | |   |   | |  |||  |    | ||| | |   | | |      |  | | || |  |  |||       || ||||| || |||||||||||||| |||||| | ||||| ||||| ||||| ||||| |||||||||
gtatgctctctcttccaccctggttcaaagttgaattggtgtattgctatatcatttacctagattttcttttctttgtctacttagttaactttattatatcttttgttattttagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 10
gtacggctctgtactctctttctctcattctctctc----tttgactaacctactg-aagagtgcttatatcaattttc-----------------gataac----aggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
         | | |||||| |||  ||  ||   ||    ||  | | |  || || || |    |||  |  ||||||                 | ||||       | | ||||   | ||  || ||||| || |||||||||||||| |||||| | || || ||||| ||||| ||||| |||||||||
--------gtatgctctctctcttccaccctggttcaaagttgaattgatgtattgcaatatcatttacctagattttcttttctttctctacttagttaactttactatatcttttgttattt-tagATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAGGCTTGGCGTTGTGTGTGGCACATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------------------------------------------------------gtacggctctgtactc---tctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgt---gttttcc-cact--tgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
                                                                                       |||    |   || ||   | ||| |  |||    |   | ||  |   ||   ||   |   ||    |  | | |  |   |||  |   ||||||  || |  | ||| ||||| || |||||||| ||||| || ||| | ||||| ||||| ||||| |||||||||||||||
gtatgctttctctctgttctccctctcttgcatatctggtgtgcgtgaatttgtctttatgagtgttaaaacatgcataaacacaatgtaaaaataaatattcaaatatttgtaacatagggtaaatatg--ttgtcttgggacttgcattttctcccctctcccctcttaggcttacagttttctacattaattcagATTTGTGGAAATTATGGCCCCTGTCTTCTCTCGGGAAGCTTGGCGTTGTGTGTGGCATATGATTCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 10
---gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattt-tcgataacaggtgtgttttcccac-ttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
       | | |   ||      ||      |   |   |  ||         |         |  ||    ||| | | | || |  |  || | | |  | |||||||||||||||| |||||||| || |||||  || |||||||||| || || ||| | || || |||
gtaactagccaccaaacaaagcatcatgtgatgggttcataagatggcttccttttttgagattcgtactcgtttgttggtcactgacggattgttcgatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG

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|86085178|gb|DR380937.1|DR380937
EST:     AAGGAAAAACCAGGATGGTGCAGTGATCCACATTTACCTCCATGTGCTGC                         GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGT
genomic: AAGGAAAAACCAGGATGGTGCAGTGATCCACATTTACCTCCATGTGCTGCgtacggctct ... ccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
                          cgataac  putative branch site (score: 3)
                                        ttttcccactt  putative PPT
             ttatatcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC