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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgaaaaaacatccattgcacttgcacatatctaagcgtaacatgaaatctcaaaaatcctttcttgttgactataacatcactctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG

Basic information

species Arabidopsis thaliana
transcript AT5G65620.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 10
gtaaatgaaaaaacatccattgcacttgcacatatctaagcgtaac--atgaaatctcaaaaatcctttcttg-ttgactataacat-cact--ctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG
     ||| |||| ||| | ||   |   || |  || |    ||       ||| |    | |  | | |   || | |||    | ||||  ||  ||  ||||| ||||| || || ||||||||||| ||||||||||| || |||||||| ||||| |||||||| || |||||||||||  ||   || |||||||| |
-----tgataaaatatcaactgatataatacgttactcactagaattagcctaatttgtgcacttatctataaattcattatggtttacactatctttttctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCTCTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG

upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 10
-gtaaatgaaaaaac---atccattgcacttgcacatatctaagcg-taacatgaaatctcaaaaatcctttcttgttgactataacatcactctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG
 || | ||  ||  |   ||| || | | |  |  | || |  ||  | |  |  ||  ||| ||   ||| |    |   | |    ||| | |   |  ||||| ||||| || || ||||||||||| ||||| ||||| || |||||||| ||||| |||||||| || |||||||||||  ||   || |||||||| |
cgttactggcaattcttaatctatagaattatccta-atttgtgcacttatctataaattcataatggcttacactatctttttcttttcatttt---tctcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAACATATGCTTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATG

upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 13
gtaaatgaaaaaacatccattgcacttgcacatatctaagcgtaacatgaaatct---caaaaatcctttcttgttgactataacatcactctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG
  |   |     |      ||    ||  |||||    | | |    |  | | |   ||   |   | |  | |||      | ||     || ||| ||||| ||||| || || ||||||||||| ||||| |||||||| |||||||| |||||||||||||| || ||| ||||||| ||    || |||||||| |
--agtgggggtgatggtggttatgtttatacatagaatatcatcttgttcagtttgtgcatgcacaatcttatattgttagatatatatgcatgttttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG

upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 10
gtaaatgaaaaaacatccattgcacttgcacatatctaagcgtaacatgaaatct---caaaaatcctttcttgttgactataacatcactctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG
  |   |     |      ||    ||  |||||    | | |    |  | | |   ||       | |  | |||      | ||     || ||| ||||| ||||| || || ||||||||||| ||||| |||||||| |||||||| |||||||||||||| || ||| ||||||| ||    || |||||||| |
--agtgggggtgatggtggttatgtttatacatagaatatcatcttgttcagtttgtgcatgcgcaatcttatattgttagatatatatgcatgttttgcagGTTGAGACTGTTTTCCATGAATTTGGTCATGCACTTCAGCATATGCTTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATG

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|86065054|gb|DR360811.1|DR360811
EST:     ACCAAACTCCACCAGTAGGTGACAAGCCAAGCCTTATGACATTCCGTGAG                         -TAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCCACATGCTT
genomic: ACCAAACTCCACCAGTAGGTGACAAGCCAAGCCTTATGACATTCCGTGAGgtaaatgaaa ... tgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGC-ACATGCTT
EST: gi|86065055|gb|DR360812.1|DR360812
EST:     ACCAAACTCCACCAGTAGGTGACAAGCCAAGCCTTATGACATTCCGTGAG                         GTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACG
genomic: ACCAAACTCCACCAGTAGGTGACAAGCCAAGCCTTATGACATTCCGTGAGgtaaatgaaa ... tgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgaaatctcaaaaatcctttcttgttgactataacatcactctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG
                                       tcactct  CT-rich tract
          tcaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgaaaaaacatccattgcacttgcacatatctaagcgtaacatgaaatctcaaaaatcctttcttgttgactataacatcactctgatttacagGTAGAGACAGTATTTCATGAATTTGGACATGCTCTTCAGCACATGCTTACGAAGCAGGATGAGGGGCTAGTTGCTGGTATCCGAAATATCGAGTGGGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG