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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctcttctcattctaaatttgcatattgttcatacaaatcggacatttgatctgattgtttctcataaattag

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 11
TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctcttctcattctaaatttgcatattgttcatacaaatcggacatttgatctgattgtttctcataaattag
||||| || |||||  |||| || |||||||| |||||||||||||||||||||||||| ||||| |   ||     | |||||| |   |||   || |                                         
TACTCTAATTCTGACACTGTGGTTTATGTTGGATGTGGAGAGAGAGGAAATGAAATGGCAGAGgtttggttc-----aatctaaaatacaataaaatttag----------------------------------------

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 11
TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatc----tcttctcattctaaatttgcatatt--gttcatacaaatcggacatttgatctgattgtttctca-taaattag
||||| || || ||  |||| || ||||||||||||||||| ||||||||||||||||| ||||| | ||    ||||||| ||  ||   |    | |  |||   |||  | ||| ||||    |    ||| || | | | | ||
TACTCTAATTCAGACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGAAATGAAATGGCGGAGgtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcag

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 11
TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtat-atctcttctcattctaaatttgcat----attgttcatacaaatcggacatttg---atctgattgt---ttctcataaattag------------------------------------------------------------------
|| ||||||||  |||||||||| || ||||||||||||||| | || ||||||||||||||||| | || |  |  | ||||      |||     |||  |    |   | |||| |||    | ||  |||    ||||  |   | |                                                                   
TATTCCAACTCCAATGCTGTTGTTTACGTTGGTTGTGGAGAGCGTGGGAATGAAATGGCTGAGgtgtgatattatgaccttctgggccagcaattaaattacttgagctttttggacgtttataaagctacttgcgcgttcttgttcgtcaagtggagtattgtatgaagtgcttctctaggggcgtatactgaacatccttgggttgctgtatgtag

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 11
TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctcttctca-------ttct--aaatttgcatattgttcatacaaatcggacatttgatctgattgtttctcataaattag----------------------------------------------------------------------------------------------
|| ||||||||| |||||||||| |||||||| ||||||||| | || ||||||||||||||||| |     | |          ||||  ||   ||  | |   |  || ||    |    ||| | |  ||    ||  |  ||||                                                                                               
TATTCCAACTCTAATGCTGTTGTCTATGTTGGCTGTGGAGAGCGTGGGAATGAAATGGCTGAGgtgtggtcttgcctggacaattttcttgaagcatgggtttcaattttataacaatgtgtattgctgttgttaaaacttgtgcattatcaagttgtcttgctacatcatatttttgagtgtggtaatacgataatatttcatgccatggtatgtagttaactgttggagctgtggtgtgtag

upper sequence: AT1G78900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 11
TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgt------atatctcttctcattctaaatttg----catattgttcatacaaatcggacatttg---atctgatt-----gtttctcataaattag-------------------------------------------------------------------------
|||||||||||  |||| ||||| || || || ||||||||| | ||||||||||||||||||||      || |  |      |||     | |    || ||||||||| |    ||||  |||    |||||| |      ||  || ||    ||                                                                         
TACTCCAACTCCAATGCAGTTGTTTACGTCGGCTGTGGAGAGCGTGGAAATGAAATGGCTGAGgtttcgtaatgtgaccataacttccttgctcgtaatcaaattgttcat-ctttgcggatgtttacgaatctgactcagggattcttcctattgcagtggggtatctcatgaactcaaagtttgcttctccaaatttatgtaaccaatttgtttggcttgtggtgtgtag

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|116463760|gb|EG506352.1|EG506352
EST:     ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCGTGATGGCCGTGAG
genomic: ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
EST: gi|164211749|gb|ES085155.1|ES085155
EST:     ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
genomic: ATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
EST: gi|116482299|gb|EG524891.1|EG524891
EST:     ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATG
genomic: ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATG
EST: gi|124960584|gb|EL035242.1|EL035242
EST:     TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAAATGACGTTGCCTGATGGCCGTGA
genomic: TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAA-TGACGTTGCCTGATGGCCGTGA
EST: gi|124754717|gb|EH844847.1|EH844847
EST:     GTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAA
genomic: GTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAA
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
genomic: ATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
EST: gi|125100559|gb|EL155962.1|EL155962
EST:     TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG                         GTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG
genomic: TTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctct ... cataaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAGgtatatctcttctcattctaaatttgcatattgttcatacaaatcggacatttgatctgattgtttctcataaattag

- - - - - -  ATGCTG
- - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - AGAGGA