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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG

Basic information

species Arabidopsis thaliana
transcript AT4G09800.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g07719.1 (Oryza sativa), 3'ss of exon 2
--------gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaa--acatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
           | | | ||   |    |   | |    |   |  ||| | ||| | |||   |    ||||    |||     |  |||   || |    || |||||||||||| |  | || |||||||||||||||||| | || || |||||||||||||||||  | || ||||||||||| |||||||| ||||||
cgaggctttggactgctaacttctttgggctaattaattgcattctcagagttgaacaaattgctctttgatttcatttgaactaccttttgtaatt---cagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGTGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 3'ss of exon 3
--gtaaatacaaaaaccaacagataattc---ttatctttgttcacaattgcataaaacatggtg-ataatgtttctttcatgtttgacaaatgg-atagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
   |   | ||     |  |  |||||     ||||  |  | |  |  || |  ||||||||   |   ||  ||   |   |        |     || |||||||||||| |  | || |||||||||||||||||| | || || |||||||||||||||||  | || ||||||||||| |||||||| ||||||
tgtttctttcagcttactcccaataatctagattataataatcccaagctgaaagaaacatggcctaagttgaatcgaactactccattttgtaatgcagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGCGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g07770.1 (Oryza sativa), 3'ss of exon 2
------------gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
            |||    || |    |||| ||    |||   |||  |   || | | ||  |  |  |  ||||    |  |    |||   || |    || |||||||||||| |  | || |||||||||||||||||| | || || |||||||||||||||||  | || ||||||||||| |||||||| ||||||
cgagtactttttgtattctcacagttgaacaaattgcgctttgatttcatttgaactac-tacgat-taattgtaatcgaaccatatctttttgtaatt---cagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGTGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 3
-----------gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
               || ||  |   |   |||   | | |  | |||| || ||    ||     |  | |   |    ||  | ||||       || | || |||||||||||| ||||||| |||||||| ||||||||  | || || ||||||||||| || ||  | || || |||||||| ||||| || ||||||
gtttgttacccaggcattcatcatgtattggatccctttaacttatgttgaccatcttttacgctctcatcacccttgcgctcacttgttcct----tgtacagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTGCGTGGGCAGCACACCAAGACAACCGGAAGGAGGGGTAAGACTGTCGGTGTGTCCAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G130544_T02 (Zea mays), 3'ss of exon 3
gtaaatacaaaaaccaacagataattcttatctttgt-tcacaattgcataa----aacatggtgataat---gtttctttcatgtttgacaaatgg-atagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
||  ||      ||   |  | | |    ||  |||  ||   | | ||| |    |  || ||  ||     |    |   || ||| |    |     || |||||||||||| || | || |||||||| ||||| ||| | || || |||||||||||||||||| |  | |||||||| ||||||||||| ||||||
gtccat-tgtgcactgtct-acactctacattcttgcatcgagaatacatgatcttattatcgtagtagcccagaccttcagatttttaatttgttctgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGCGTCCGTGGCCAGCACACCAAGACTACTGGTAGGCGTGGAAAGACCGTTGGTGTCTCCAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
-----------gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
            | ||     |||       ||  | | | || ||||| |    || |      | | | | | |      |||   | |      |    || |||||||||||| || | || |||||||| ||||||||| | || || ||||||||||| |||||  |  | ||||| |||||||||||||| ||||||
tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgttta----tgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G062911_T01 (Zea mays), 3'ss of exon 3
-gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggat-------agAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
  |  ||       |  |    | ||    |  | |    | | |||| |      || |  |  |||||  |    |    | ||     |       || |||||||| ||| |  | || |||| ||| || ||||||   || || |||||||||||||||||  |  | ||||||||||||||||| |||||||||
ttttcatttgtgttcgtaactgttatatgcacttctcccaaaatttgcttgcggtttg-tagttgtgttttgtatgcgacacagaaccttgtgttatccagGAACCACCGAGGTCTCCGTCACTACTAGGGCCTGCGTGTCCATGGCCAGCACACCAAGACTACTGGAAGGCGTGGAAAGACTGTTGGTGTGTCAAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G36610.2 (Glycine max), 3'ss of exon 3
--gtaaatacaa------aaaccaacagataattcttat-ctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
  || |||| ||         ||  ||   | |   ||| | |||||    |||| | || |   | | |  |  |    ||      | || | |    |||||||||||||||||||||||||||||||| || |||||| | || || ||||||||||||||||| || || |||||||||||||||||||| ||||||
ttgttaataaaatccttgttgccctcaagcattgtgtatgcattgtttg--attgaaaaacattggctaacgaactgaaattgtatccttactattatgcagAAACCACCGTGGTTTGAGGCATTACTGGGGCCTTCGTGTCCGTGGTCAGCACACCAAGACTACTGGCCGTAGGGGAAAGACTGTTGGTGTCTCTAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G30970.1 (Glycine max), 3'ss of exon 3
-gtaaatacaaaaaccaacagataattct--tatctttgttcac--aattgcataaaacatgg-tgataatgtttctttcatgtttg-acaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
   || |        |  |||||  || |     | ||||   |   |||  | |||   ||| | || |  |     |||| |    || | |    ||||||||||||||||||||||| |||||||| || |||||| | || || ||||||||||||||||| ||||| |||||||||||||| ||||| ||||||
taaaattctggttgtcctcagatttttgtgtgggcattgtctgcctgattaaaaaaatattggctaatgagctgaaaatcatatccctactattatgcagAAACCACCGTGGTTTGAGGCACTACTGGGGCCTTCGTGTCCGTGGTCAGCACACCAAGACTACTGGCCGCAGGGGAAAGACTGTTGGGGTCTCTAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G08690.1 (Glycine max), 3'ss of exon 3
-gtaaatacaaaaacc-aacagataattcttat--ctttgttcacaattgcataaaacatggtgataatgtttctttcatg---tttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
  |   | | |   |  || ||    |  || |  | ||||| |    ||||||  |   ||| ||||   |    || ||   | | || | |    ||||| ||||||||||||||||| ||||||||||| |||||  | || || ||||| ||||||||||||||||| || || |||||||||||||| ||||||
atttcctgctacttcttaatagggtctctttgtgcccttgttaagttgtgcatattattaggtaataacactaacatcttgtattcttactattatgcagAAATCACCGTGGTTTGAGGCACTACTGGGGTCTTCGTGTTCGTGGTCAGCACACTAAGACTACTGGTCGCAGGGGTAAAACTGTTGGTGTCTCTAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G36880.2 (Glycine max), 3'ss of exon 3
--------------gtaaatacaaaaaccaacagata-attcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
               |||| ||  | |  || | ||  |  |  || |    | ||  ||  || |||     ||| | || |  ||  ||  |||          || ||||| ||||||||||| || ||||||||||| |||||  | || || || |||||||| |||||||| || || || ||||||||||| || ||||||
cttcatttgttttcataaaaacgtatagaaatatatggaaacacatgtcaaattact-ttctattaaatccaatgaaattgatattt--atacttg-----catgcagGAACCATCGTGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCCAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 3
----gtaaatacaaaaaccaacaga--taattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggat--agAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
     |   | |    | | |  ||  |   | |||| ||   |    |  |  |||||||||  |||    |   | |    ||| |    || ||  || ||||| || |||||||| || ||||||||||| |||||  | || || || |||||||| |||||||| || || || ||||||||||| || ||||||
tcctctgcttccgttcatctatggaccttgattttatattctgttgtcagagagtaaaacatga-gattgcatccttattgatttttattcttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCATACCAAGACCACTGGTCGTAGGGGTAAAACTGTTGGTGTGTCTAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttg-acaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
        ||    |           ||    || | |     ||| |    |   |     |   ||||| | ||    | || ||   ||   |    || |||||||||||| ||||||| |||||||| ||||||||  | || || ||||||||||| || ||||| ||||||||||||||||||||||| ||||||
agggcaccgtgtccattgtttgtggtagtaggttgtgaatgaagttta-ggctaggtggggaaacatgatact-ttcagctaatcttgatactgttatgcagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCACACCAAGACCACAGGTCGTAGAGGAAAGACTGTTGGTGTCTCTAAGAAG

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|164120484|gb|ES098220.1|ES098220
EST:     GACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
genomic: GACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
EST: gi|125279078|gb|EL293163.1|EL293163
EST:     GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAG
genomic: GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAG
EST: gi|124967313|gb|EL041356.1|EL041356
EST:     AGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
genomic: AGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
EST: gi|164084888|gb|ES163099.1|ES163099
EST:     GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTG
genomic: GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTG
EST: gi|86077988|gb|DR373745.1|DR373745
EST:     GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
genomic: GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
EST: gi|124735476|gb|EH826878.1|EH826878
EST:     ATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
genomic: ATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
EST: gi|116431165|gb|EG473757.1|EG473757
EST:     GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
genomic: GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
EST: gi|163965896|gb|ES156640.1|ES156640
EST:     ACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCA
genomic: ACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCA
EST: gi|164041773|gb|ES139665.1|ES139665
EST:     AGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCACCGTGGTTTGAGGCATTACTGGGGTC
genomic: AGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTC
EST: gi|86081140|gb|DR376897.1|DR376897
EST:     GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAG                         AAACCMCCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA
genomic: GCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaa ... aaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG
                                      gtttgac  putative branch site (score: 4)
         ataaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatagAAACCACCGTGGTTTGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGACTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG