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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtaaagttgattgctttacatgaaactgtgtactgattgtgtatgcatttgattgatgttttaatgtgaattttcatggttttggttgattgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT

Basic information

species Arabidopsis thaliana
transcript AT5G03850.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G124143_T03 (Zea mays), 3'ss of exon 1
ctgtaaagttgattgctttacatgaaactgtgtactgattgtgtatgcatttgattga--tgttttaatgtgaattttcatggttttggttgattgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT
 |||      | ||    | ||  || |||||   |||     | ||      |  |   || || |   |||    | |    |    |  |      ||| |||||  | ||  | ||||  ||||| ||||| ||||| ||||| ||||| || || |||||||||||||| |||||  ||||||||||    ||    
ttgtttgccagtttctacttca--aagctgtgatttgaggaactttgtgaacaaagggcctgattcaccttgacaactgacaaatgctttctacaagtgcagTATGGACACCCAAGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGAAGGACCGGCTCCAGGGGTCAGGTTACCCAGGTCAGAGTGAAGTTCTTGGATGAC

upper sequence: AT5G03850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
-ctgtaa-agttgattgctttacatgaaactgtgtactgattgtgtatgcatttgattgatgttttaatgtgaattttcatggttttggttgattgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT
 | |||  |    |     | |||    | |    |   | | |||   ||    ||  ||| || |   ||| |  | |    |    |  ||| |  ||| |||||  | ||| | ||||  ||||| ||||| ||||| ||||| ||||| || || ||||||||||| || |||||  |||||||||||   ||    
ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagcat--atggttcaccttgattactgacaaatgctttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC

upper sequence: AT5G03850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
ctgtaaagttgattgcttt--acatgaaactgtgtactgattgtgtatgcatt--tgattgatgttttaatgtgaattttcatggttttggttgattgaat--cagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT
   | |  ||| ||   |   || |||||      ||  |||   |    | |  || ||  | |||     | |          ||||  |||   | |   |  ||||||| |   | | ||||| ||||||||||| || || |||||| | ||||| |||||||||||||| || |||||  |||||||||||   |     
-aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----

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|125307462|gb|EL321547.1|EL321547
EST:     AACCTTCATCTACAG                         AATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
genomic: AACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
EST: gi|86077841|gb|DR373598.1|DR373598
EST:     TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAG                         AATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
genomic: TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
EST: gi|86076184|gb|DR371941.1|DR371941
EST:     TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAG                         AATGGATTCTCAGATCAAGCGCGCTGTGGTGGTTAAGGTCATGGGTAGGAC
genomic: TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
EST: gi|124713801|gb|EH805203.1|EH805203
EST:     CGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAG                         AATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
genomic: CGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
EST: gi|152038477|gb|AV823992.2|AV823992
EST:     TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAG                         AATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
genomic: TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
EST: gi|164095723|gb|ES135307.1|ES135307
EST:     CAACCTTCATCTACAG                         AATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
genomic: CAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGAC
EST: gi|164086887|gb|EL989257.1|EL989257
EST:     TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAG                         AATGGATTCTC
genomic: TTTTTGCCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTC
EST: gi|124936878|gb|EL013717.1|EL013717
EST:     CCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAG                         AATGGATTCTCAGATCAAG
genomic: CCTCTCACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGATCAAG
EST: gi|124838132|gb|EH922571.1|EH922571
EST:     CACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAG                         AATGGATTCTCAGA
genomic: CACGCTTATCGCCGCATCTCCGTCAACCTTCATCTACAGgtatcttcat ... attgaatcagAATGGATTCTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttgattgatgttttaatgtgaattttcatggttttggttgattgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT
               ttttaatgtgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtaaagttgattgctttacatgaaactgtgtactgattgtgtatgcatttgattgatgttttaatgtgaattttcatggttttggttgattgaatcagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT

- - - - - - - - - - -atgaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg