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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACAAAAGATCTTCATTGAGTACATAATGCTTGATGGAGTAAATGATCAAGAGCAGCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTGgtaaatcttcgatgtcttaatactcttaaaggttctgcaattatctgatgatattttttatggaaactctgtgctcttttcttgaacag

Basic information

species Arabidopsis thaliana
transcript AT3G19630.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G19630.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g10520.1 (Oryza sativa), 5'ss of exon 7
TCAACAAAAGATCTTCATTGAGTACATAATGCTTGATGGAGTAAATGATCAAGAGCAGCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTGgtaa--atcttcgatgtcttaatactcttaaaggttctgcaattatctgatgatattttttatggaaactctgtgctcttttcttgaacag-----------
  | || |  ||||| ||||||||||| |||||||||||||| || ||||| |||||||| || || |  || ||  |||| ||  | |  ||| ||| |||||  | |||     ||||  | ||        | |||  ||||||| || |    || | |  ||    ||       ||| ||| ||            
CAAGCAGACCATCTTTATTGAGTACATCATGCTTGATGGAGTTAACGATCAGGAGCAGCATGCCCACCAGCTTGGTAAATTACTTGAAATGTTTAAAGCGgtaagaaactttctgttctttctgcttcatttcatcctg--attatcttattaatgattcttttaaatggttggaaaaccttcctgatcatctttgcggtat

upper sequence: AT3G19630.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G119104_T01 (Zea mays), 5'ss of exon 7
TCAACAAAAGATCTTCATTGAGTACATAATGCTTGATGGAGTAAATGATCAAGAGCAGCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTGgtaaatcttcgatgtcttaatac--tcttaaaggttctgcaattatctgatgatattttttatggaaactctgtgctcttt-tcttgaacag--------
| | || |  |||||||||||||| || |||||||||||||| || ||||| ||| |||| || ||||  || ||  || ||||  | || ||| ||| ||| |  |         ||| | |  | |||    |  | |  |  |||  |    || ||   |  |  ||| ||  |    | |  ||||         
TAAGCAGACCATCTTCATTGAGTATATTATGCTTGATGGAGTTAACGATCAGGAGGAGCATGCACATCAGCTTGGTAAACTGCTTGAAACGTTTAAAGCGgtgagacactatcacattactgcatttttatcattattaccttgctctagttcctttcttctagtcacttctttgtaccagatgtctaacaccaattttg

upper sequence: AT3G19630.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv03s0091g00820.t01 (Vitis vinifera), 5'ss of exon 6
TCAACAAAAGATCTTCATTGAGTACATAATGCTTGATGGAGTAAATGATCAAGAGCAGCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTGgtaaatcttcgatgtc---ttaatactcttaaaggttctgcaattatctgatgatattttttatggaaactctgtgctcttttct-tgaacag-----------
|  ||| || ||||| ||||||||||||||||||||||  || |||||| ||||||| || ||||| |  || ||  |||||||  ||||||||||||||||||    |  || ||   ||| | |    | |   |||||  | |||  ||| | |||  |||| | | | ||     |||||  |     |           
TGGACAGAAAATCTTTATTGAGTACATAATGCTTGATGAGGTGAATGATGAAGAGCAACATGCTCACCAGCTTGGGAAATTGCTGGAGACATTTCAAGTGgtaagatctatatttcaaattactgcatgcagaaactctgct-tcatc--atgct-tttgctatgaagagtgtgcatatttttcaatatgtggattactgatta

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|86080780|gb|DR376537.1|DR376537
EST:     GCACGCTCATCTACTAGGCGAATTGCTAAAGMCATTTCAAGTG                         GTCATAAATTTGATACCATTTAATCCAATTGGATCCACAAGCCAATTCGAA
genomic: GCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTGgtaaatcttc ... tcttgaacagGTCATAAATTTGATACCATTTAATCCAATTGGATCCACAAGCCAATTCGAA
EST: gi|164025090|gb|ES192392.1|ES192392
EST:     AAGAGCAGCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTG                         GTCATAAATTTG
genomic: AAGAGCAGCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTGgtaaatcttc ... tcttgaacagGTCATAAATTTG
EST: gi|19742348|gb|AU227701.1|AU227701
EST:     GAATTGCTAAAGACATTTCAAGTG                         GTCATAAATTTGATACCATTTAATCCAAGTTGGATCCACAAGCCAATTCGA
genomic: GAATTGCTAAAGACATTTCAAGTGgtaaatcttc ... tcttgaacagGTCATAAATTTGATACCATTTAATCCAA-TTGGATCCACAAGCCAATTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACAAAAGATCTTCATTGAGTACATAATGCTTGATGGAGTAAATGATCAAGAGCAGCACGCTCATCTACTAGGCGAATTGCTAAAGACATTTCAAGTGgtaaatcttcgatgtcttaatactcttaaaggttctgcaattatctgatgatattttttatggaaactctgtgctcttttcttgaacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG