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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactctatttccattcaaaaaaactttccctattttcttttatgtctcaatcatttgctactttctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG

Basic information

species Arabidopsis thaliana
transcript AT5G30510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 5
gtaactctatttccattcaaaaaaactttccctattttcttt----tatgtctcaatc-atttgctactttctgctgtctcaa----gGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
||||     |||  |  ||| |   |||   ||  |   | |    | | |   ||   |  | ||  ||||| |||||||||    |||||| ||||||||||||| |||||| ||||| || || |||||||| || ||||||||||| || ||| |  | ||||| ||||||
gtaa----gtttgaaagcaatattccttgatctggtccatctggaatgtatacaaactgacatactgttttct-ctgtctcaaaacagGCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 5
-------gtaactctatttccattcaaaaaaactttccctat-tttcttttatgtctcaatcatttgctactttctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
         |||   |    ||||     |     |   |||  ||    || |   |   ||| || |   || ||||      ||||||| ||||||||||||| |||||| |||||||| || || ||||| || ||||||||||| |||||| |  | ||||| || |||
gtaagaataaacaaaagcaacattttctcatgtgctgaatatgctttaggtaagcaactgacatatggtttcttttgctcaaattagGCTGATGAGATGGCTCAGATATTCAGGCAGAGAATAGCTCAGGCAGAGGCTATGGCTCGTGCTGACATGTTGAGATTCCAGCCAGAG

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G04190.1 (Glycine max), 3'ss of exon 5
---------------gtaactctatttccattcaaaaaaactttccctattttcttttatgt----ctcaatcatttgctacttt-ctgctgtctca-agGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
                ||| |||| ||| |  ||       |  |  |    | ||| | |      | | |||  |  | |||  ||  | | | | |||| |||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||  | ||||| ||||||
catcacttacatgttttaaatctaattcaacccatttctgttagcattggaatttttgaaggagaatttactcacataatccttaacttttttgttatagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATAGCCCAAGCAGAAGCTATGGCTCGTGCAGACATGCTAAGGTTCCAGCCTGAG

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 5
----------------gtaactctatttccattcaaaaaaactttccctattttcttttatgt----ctcaatcatttgctactt--tctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
                   |||  |   |  ||||  |  | | ||  |||  | ||| |         ||  | | |  | |||  |||| ||| | ||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||| | ||||| || |||
tctatgtttttaatcatctacttcaacccttttcattagcattatcattatcatttttgaaagagaatgcacacttataattcttaatctgttgt-taaagGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 5
----------------gtaactctatttccattcaaaaaaactttccctattttcttttatgt------ctcaatcatttgctactttctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
                   |||  |   |  ||    |  | | ||  ||   | ||| |         | || | || |       |||| |||   | ||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||| | ||||| || |||
tctatgtttttaatcatctacttcaaccctttttgttatcattatcattaccatttttgaaagagaatgcacagttatatttcttaatctgttgttata-gGCGGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCTCAAGCAGAAGCTATGGCTCGTGCTGATATGCTTAGATTCCAGCCAGAG

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 3'ss of exon 5
----gtaactctattt-----ccattcaaaaaaactttccctattttcttttatgtctcaatcatttgctactttctg----------ctgtctcaa--gGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
    || |||  |  |     |||  ||       |   ||| |     |||      || | ||||   | |   ||          ||||   ||  ||| ||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| |||||||||||  | ||||||||||||
ttctgttacttcacctataaaccacacatgtgtgttgctcctctacctatttgaaatccagtgatttaacaatacttggctcttaaccctgttctaacagGCGGAGGAGATGGCTCAGACATTCAGGCAGAGAATAGCTCAAGCAGAAGCTATGGCTCGGGCAGACATGCTAAGATTCCAACCTGAG

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|125249089|gb|EL263174.1|EL263174
EST:     GCCAACACCTGGTGATATGATTCGTAACCCAAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGG
genomic: GCCAACACCTGGTGATATGATTCGTAACCCAAAA-CTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGG
EST: gi|164149448|gb|EL988213.1|EL988213
EST:     CCTGGTGATATGATTCGTAACCCAAAACTTGTGTTTCGAGAAG                         GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGC
genomic: CCTGGTGATATGATTCGTAACCCAAAACTTGTG-TTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGC
EST: gi|125279320|gb|EL293405.1|EL293405
EST:     CGTAACCCAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
genomic: CGTAACCCAAAACTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
EST: gi|125308295|gb|EL322380.1|EL322380
EST:     TGTGTTCGAGAAG                         GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
genomic: TGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
EST: gi|125044858|gb|EL117127.1|EL117127
EST:     GCCAACACCTGGTGATATGATTCGTAACCCAAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGG
genomic: GCCAACACCTGGTGATATGATTCGTAACCCAAAA-CTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGG
EST: gi|86074980|gb|DR370737.1|DR370737
EST:     AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
genomic: AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
EST: gi|125050784|gb|EL123053.1|EL123053
EST:     AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGG
genomic: AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGG
EST: gi|125176717|gb|EL196018.1|EL196018
EST:     AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGGCTCA
genomic: AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGGCTCA
EST: gi|125229112|gb|EL243197.1|EL243197
EST:     GTAACCCAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
genomic: GTAACCCAAAACTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
EST: gi|124812181|gb|EH897047.1|EH897047
EST:     ATTCGTAACCCAAAACTTGTGTTCGAGAAG                         GCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
genomic: ATTCGTAACCCAAAACTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCC
EST: gi|124766480|gb|EH856610.1|EH856610
EST:     AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAG                         GCTGAGGAGAT
genomic: AGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTGTGTTCGAGAAGgtaactctat ... ctgtctcaagGCTGAGGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttccctattttcttttatgtctcaatcatttgctactttctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG
                                      ctttctgctgtctc  CT-rich tract
        tattttcttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactctatttccattcaaaaaaactttccctattttcttttatgtctcaatcatttgctactttctgctgtctcaagGCTGAGGAGATGGCTCAGACATTCAGACAGAGAATTGCGCAAGCAGAAGCCATGGCTCGTGCAGACATGCTTCGCTTCCAACCTGAG

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