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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC

Basic information

species Arabidopsis thaliana
transcript AT3G02780.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
-gttgctatgat-gatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttct-tctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC
  ||   ||| |  |  ||| | | |  |  || ||  |  ||  | |    |   |   |       |   ||||||     | ||| |     ||   |||||| | ||    ||||||||||| || |||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||| ||||| ||    |
tcttcaaatgctcaactggaagttatttt--tcatatctcatttctag-cactgccatcttattcttcaaaacatctgctgattatctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G108285_T01 (Zea mays), 3'ss of exon 3
gttgctatgatgatgggatgctctcgtg-atcgtagatggttggt-gggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC
  |  ||  ||| | |  || | | |   | |  |      || | | |  |     ||     ||| ||    | |||   || || |     | |  |||||||||||    ||||||||||| || ||| |||| ||||| || || || |||||||| ||||| |||||||| || |||||||||||||| ||    |
-gtatta-aatgtttgtttgtttttgaacaacacattccaatgtttgtgactatcctattcttttcaaattgtttttgataagtatcattctactcgtgcagCAAAGGTCCGCGACAAAGGTTACCTTTCCTTTAGTTTGGACCAATACCTGCTGCAGCCACCCTCTGTACCGTGAGTCTGAGCTTATCCAGGAGAACTACC

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 3
---gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC
   ||    |      |  | |||    ||  |   |  |  |||    || ||  |||| |||    | ||  |      |  ||| ||||   |     ||||| | ||    |||||||| || |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||| ||||||||  | || ||||| |
ttggtgaaaaattctctatgttgcatgtgtattttcaagtctttgactcgtgttt-taatttggtctgtttg--actgagattctttgttctttatgatgaagCAACGATCTGCAACAAAGGTAACTTTCCCTCTTGTGTGGACAAACACCTGTTGTAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCC

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
--gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC-
  || |  ||     |  |   |    ||  |   |  |  | |    ||  |  |||| |||    | ||  |      |   || ||||   |     ||||| | ||    || ||||| || |||||||| |||||||| ||||| |||||||||||||| || ||||||||||| ||||||||  | || ||||| | 
tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctt-taatttggtctctttg--actgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0206g00020.t01 (Vitis vinifera), 3'ss of exon 1
gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC---------------------
             | ||| |||  || |  | ||  | |       || ||     | |  ||||   | | | | | |  ||| |  |   |       ||||   |     ||       | | | || ||  ||| |  |   ||| ||   |  |   |  ||   |||    |      |   || |   |                         
-----------tttcggaggctgacgagggcttactttgc-----agtcttggaggtttcactcaacagccgtgttattcttttatattgaatctggatacaaacacctgctgcagC-----CATCCTCTTTACCGTGAATCAGATCTTATTAATGAGAATGTGCTTGGAGTGCGGAATGCTGCACAAAGAAAGCTATTGGGTGAACTCGGCATTCCTGCT

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 3
gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaat---aatctggc--tcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC
     | |        ||| || ||  |||     ||  || ||     | |     ||| ||    ||| |||   | |  ||   | | | |   ||| ||||||||||||   ||||||||| || |||||| | |||||||| ||||| || |||||||||||||||||||||||||||||||||||  | || ||||| |
----ttgtttcaccctgattctatcaagatatagcattctttgtaaacatcagccagaatttgagaatcacatgctgtgtt-ctttctgcatgtttcttgtacagCAAAGGTCTGCCACAAAGGTGACATTCCCTTTGGTGTGGACAAACACCTGCTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATTGATGAGAATGCGC

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S28_399V6.1 (Physcomitrella patens), 3'ss of exon 3
--gttgc-tatgatgatgggatgctctcgtgatcg--tagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC-
     |  |||| | |  |  ||   | ||||  |  | |  ||   ||    ||||      |||   | || | || |   || |    |    |||   ||| || | ||    || || || || || || || |||||||| |||||||||||||||||||| || |||||||| || || |||||  |||| ||   || 
ccaccgtgtatggttagagattggattagtgagtgacttgcagggatgtctcctttagacccatggacaaaatcttattta--tgttgatattatattt---cagAAACGTTCGGCTACGAAAGTGACCTTTCCACTTGTGTGGACCAACACTTGTTGCAGCCATCCACTGTACCGTGAGTCTGAACTTATTGAGGATAA-ATACC

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ38651 (Selaginella moellendorffii), 3'ss of exon 3
gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC
                               ||    | | |     || |  | || |   |  | | ||||  || || | |    |    ||  |||||| | ||    || ||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| || || || || ||| | ||    || ||   | 
-------------------------------gtgatcgatcgagtctttcttttcatttcatt--tctctcatacgattgttgttggatttgatgcccagCAACGCTCGTCGACCAAGGTGACGTTCCCTCTGGTGTGGACGAACACATGTTGTAGCCACCCTCTCTATCGAGAGTCGGAGATGATTTTCGAGAACCAAA

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ31498 (Selaginella moellendorffii), 3'ss of exon 3
gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC
                         ||||||| |    ||   |   || |  | || |  |||||| |     ||   | |||  |  |       |||||| | ||    || ||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| || || || || ||| | ||    || ||   | 
-------------------------gtgatcg-atcgagtctttcttttcttttcatttctctcatacgattgttgttggatttgatgcc-------cagCAACGCTCGTCGACCAAGGTGACGTTCCCTCTGGTGTGGACGAACACATGTTGTAGCCACCCTCTCTATCGAGAGTCGGAGATGATTTTCGAGAACCAAA

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|47828035|gb|CK117719.1|CK117719
EST:     GGGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAG                         CAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT
genomic: GGGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAGgtatgtacat ... gtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT
EST: gi|116477195|gb|EG519787.1|EG519787
EST:     GGGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAG                         CAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT
genomic: GGGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAGgtatgtacat ... gtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT
EST: gi|116387556|gb|EG430148.1|EG430148
EST:     GGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGC-TCTTCCAG                         CAAAGGTCAAACACAAAGG-TACGTTTCCCTCTAGTGTGGACTAACACTT
genomic: GGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTC-TCCAGgtatgtacat ... gtttgaacagCAAAGGTCAAACACAAAGGTTACG-TTCCCTCTAGTGTGGACTAACACTT
EST: gi|125211187|gb|EL226141.1|EL226141
EST:     AGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAG                         CAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT
genomic: AGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAGgtatgtacat ... gtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT
EST: gi|116477196|gb|EG519788.1|EG519788
EST:     GGGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAG                         CAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT
genomic: GGGCTTTTAGTGTATTTTTATTCAACTCGAAGTATGAGTTGCTTCTCCAGgtatgtacat ... gtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC
                          atctgac  putative branch site (score: 3)
                                    tttcttctcgttt  putative PPT
     taataatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - -atgctct
- - - - - - - - - - - - - - - - - - - - - - -ggtttta