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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatcttcgactcgagtttctcttcactctgtatctcccacaattttggtctcatgttgattccatttccag

Basic information

species Arabidopsis thaliana
transcript AT3G49870.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49870.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 5'ss of exon 3
TAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatcttcgactcgagtttctcttcactctgtatctcccacaattttggtctcatgttgattccatttccag--------------------------
| || ||||| ||||| ||||| ||| | ||||||||||| || || ||||||||||| |||||||||||  | |||||||| || |||||||| ||||||||||   |||          ||   | || | || | |    |      |   |||| || | |  |||    ||                          
TGACCAAAGGTAATGTCACAATAAAATTGTGGGATCTTGGAGGCCAGCCAAGATTCCGTAGCATGTGGGAGAGATACTGTCGTGCAGTTTCTGCAATTGTgtaagttcctttcctgtctaatttgatgca-tgtgcagcaggaattgcactatactca-gtagttgtcatgcttagttggttgttgcttacacatgctaacc

upper sequence: AT3G49870.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G081622_T01 (Zea mays), 5'ss of exon 3
TAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatcttcgactcgagtttctcttcactctgtatctcccac-aattttggtctcatgttgattccatttccag-----------------------
| || ||||||||||| || || ||  | ||||||||||| || ||||||||||||||||||||||||||  | ||||| || || |||||||| |||||||| | ||      |   |  |||  ||  |  |     |  ||| |||  |   |   |||       | ||   |                       
TTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCCAACCAAGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattccattcctaaccttccattttcagtaagaatagcactaatgctcaccagctgtcatgcttagttgaggtttcttgcatacatgtctattat

upper sequence: AT3G49870.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 3
TAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatcttcgactcgagtttctcttcactctgtatctcccacaattttggtctcatgttgattccatttccag------------------------
| || ||||| ||||| || || ||| | |||||| |||| || ||||| |||||||| |||||||||||  | ||||| || || |||||||| |||||||| |  | |    | |||    |   |  |    |   |       | |||  | ||||   |||   ||   |                         
TTACCAAAGGGAATGTGACGATAAAATTGTGGGATATTGGAGGCCAACCTAGATTCCGGAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgcctttcatccccgatcaccagctgtcatgcttagttgtgtcgtcttgcacacatgcctattattttgttaagacagtgttcataccattctgata

upper sequence: AT3G49870.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S263_59V6.1 (Physcomitrella patens), 5'ss of exon 4
TAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatctt------cgactcgagtttc-tcttcactctgtatctcccacaattttggtctcatgttgattc-catttccag-----------------------------------------------------------------
| || ||||| | ||| || ||||| || |||||||| |||||||||||  | ||||| ||||||||||| || || ||||| | ||||||||  |||||||||| |  |       |||| |   |||  ||||      | |   |  | ||  ||   |   || | |  | | ||  | |                                                                 
TGACGAAAGGCAGTGTAACCATCAAGCTTTGGGATCTCGGTGGTCAACCTCGTTTCCGAAGCATGTGGGAGCGATATTGTCGTGGTGTTTCTGTAATTGTgtaagaacttgtatacgcgacacagttttgatctttgtctgggagaacttaaaaagttaagcagttgctcaagcaccttgtcggccgcctgagatgtgaatgtctacttacagattttaagcgttgagctgtcctggtaacttcttcag

upper sequence: AT3G49870.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S103_13V6.1 (Physcomitrella patens), 5'ss of exon 4
TAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatct-----tcgactcgagtttctcttcactctg-tatctcccacaattttggtctcatgttgattccatttccag-------------------------------------------------------------------
| || || || | ||| || |||||||| |||||||| ||||| |||||  ||||||| ||||||||||| ||||| ||||| | ||| ||||| |||||||||| ||||     || ||   |||||   ||  ||  | |  |||  |  |||   |  |  | |     |||||| |||                                                                   
TGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATTGTCGTGGTGTGTCTGCAATTGTgtaagaatctgtgtttccaccaaagttttggttttctgcgatggctctaaatattgaagcattttctcacgaccatttgcagtctcctgtggttcaaattttgaaagtatgtattttgaagcatttaggtgacctggtaactgtttcag

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|124847986|gb|EH932423.1|EH932423
EST:     GTTTCTGCCATTGT                         GTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGTGTGTCGAAAAGTGA
genomic: GTTTCTGCCATTGTgtaaggatct ... ccatttccagGTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGTGTGTCGAAAAGTGA
EST: gi|125105832|gb|EL159480.1|EL159480
EST:     AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGT                         GTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGT
genomic: AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatct ... ccatttccagGTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGT
EST: gi|124767423|gb|EH857553.1|EH857553
EST:     AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGT                         GTATGTAGTTGATG
genomic: AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatct ... ccatttccagGTATGTAGTTGATG
EST: gi|124773901|gb|EH864030.1|EH864030
EST:     CGCGCTGTTTCTGCCATTGT                         GTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGTGTGTCGAAAAGTGA
genomic: CGCGCTGTTTCTGCCATTGTgtaaggatct ... ccatttccagGTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGTGTGTCGAAAAGTGA
EST: gi|86072842|gb|DR368599.1|DR368599
EST:     AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGT                         GTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGTGTGTCGAAAAGTGA
genomic: AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatct ... ccatttccagGTATGTAGTTGATGCTGCAGATCCTGACAACCTAAGTGTGTCGAAAAGTGA
EST: gi|125108644|gb|EL161469.1|EL161469
EST:     AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGT                         GTATGTAGTTG
genomic: AGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatct ... ccatttccagGTATGTAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACTGTCGCGCTGTTTCTGCCATTGTgtaaggatcttcgactcgagtttctcttcactctgtatctcccacaattttggtctcatgttgattccatttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT