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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttcttctcctctaatatgtccccaaacatacatcatctactcaaaagtgaaaacattttttagccggtaattgacaacttagctatactttgtag

Basic information

species Arabidopsis thaliana
transcript AT1G19270.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G19270.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g42820.2 (Oryza sativa), 5'ss of exon 9
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttcttctcctctaatatgtccccaaacatacatcatctactcaaaagtgaaaacattttttagccggtaatt-gacaacttagctatactttgtag----
 |  ||||||||| |||| |||||||| ||| | ||||||||||||||| | || |||   |||  ||| || || || |||||||||||| ||||||||||   || |  | |||| ||| |       | |  ||  | ||  |     |||||  |  || |   | |    | || | ||  ||  ||  ||     |     
CCACATTGAATATCGGGCCCATCCTTTCTGGATGCAGAAGTATTGTCCTGCCCATGAAACTGATCGTACTCCTAGGTGCTGCAGTTGTGAACGAATGGAGgt---ttgtgctatcctataaaaaagttatacatgta-gtgattcaaatggaagtgtcaggatgt---aactaacacttcggcatgttccctcaacaaaaaaaatag

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 5'ss of exon 9
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttcttctcctctaatatgtccccaaacatacatcatctactcaaaagtgaaaacat-tttttagccggtaattgacaa--cttagctatactttgtag-
 || || |||||  | |||||||| || ||| | || ||||| |||||||| || ||| | ||||  || || || ||||||||||||||||||||||||||  ||       ||      ||  ||| |||  | ||    |   |      || |   | | ||  | |   | ||    | |   ||  |||   |||| |  
GCTGATCGAATACCGAGCACATCCATTCTGGATGCAAAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTAGGTGTTGCAGTTGTGAAAGAATGGAGgtcagtgcagggatc------tagatcctcaatgagaccagtttccccagcttgtcacttcttgttcctggaaagaaaccagccagttttgactaccatttggaaa

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G017845_T02 (Zea mays), 5'ss of exon 6
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttct------tctcctctaatatgtccccaaacatacatcatctactcaaaagtgaaaacattttttagccggtaattgacaacttagct-----atactttgtag---------
 |||||||||||||||||||||||||| ||||| || || || |||||||| || |||   |||| ||| ||||| || || |||||||||||||||||||| ||     |      | |    |||| ||  |        | ||    |  | | |||  | | | | | |  |       | ||  | ||   |     ||  |||||           
CCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCTGTAGTTGTGAAAGAATGGAGgtaggccagttagcatgtttttcttaatttggtcttgtgggcatatttcatggttagaag--agagcctctgtgtgtgaaatttggatcatttcattccaacatggtttgttcacttaccag

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G342105_T02 (Zea mays), 5'ss of exon 4
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttcttctcctctaatatg-tccccaaacatacatcatctactcaaaagtgaaaacat-tttttagccggtaattgacaacttagctatactttgtag
 || ||||||||  |||| |||||||||||| | ||||||||||||||||| || ||| | |||| ||| || || || |||||||||||| ||||||||||  || || |  |    ||  ||  |    | | ||| || || ||   | |  |  | | || || ||    | |   | | || | |  | |   |     
CCTCATTGAATACCGGGCCCATCCTTTTTGGATGCAGAAGTATTGTCCTTCCCATGAAAATGATGGTACACCTAGGTGCTGCAGTTGTGAACGAATGGAGgttagtgttatgtttacatacaataatatatatatatatat-atatatatatatatatatatatattattgatggattcataaaaaataaaatgtggatcc---

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA17G36620.1 (Glycine max), 5'ss of exon 6
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttcttctcctctaat-atgtccccaaacatacatcatctactcaaaagtgaaaacattttttagccggtaattgacaacttagctatactttgtag------------------
|||||||||||||||||||||||| || ||| | ||||| ||||| ||| |||| ||||| |||| ||| ||  | |||||||| |||||  ||||||||||  || |   |    | || | || |   |||| ||   | ||   ||       | |||  | | | | |  |||     |||  |   || | | |  |                   
TCTTATTGAATATAGGGCACATCCATTCTGGATCCAGAAATATTGCCCTACTCATGAACATGATGGTACTCCACGCTGTTGCAGCTGTGAGCGAATGGAGgtcagtatggatggagtatatttatctgatcaaatattatttatagtcttgcctagggaaaggtgtatgaacttgtacagtgcaaagtgaatacaatgtaaaattttctctccacatgcag

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA14G08450.1 (Glycine max), 5'ss of exon 7
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttt--------tcttctcctctaatatgtccccaaacata-catcatctactcaaaagtgaaaacattttttagccggtaattgacaacttagctatactttgtag------------
|||||||||||||||||||||||| || ||| | ||||| ||||| ||| |||||||||| |||| |||  |  | |||||||| || ||  ||||||||||  || |        | |  |  ||| |||       |    ||   |   |||   ||| ||| |   | || |     |  || |||  |    |  | | ||| |              
TCTTATTGAATATAGGGCACATCCATTCTGGATCCAGAAATATTGCCCTACTCACGAACATGATGGTACTACACGCTGTTGCAGCTGCGAGCGAATGGAGgttagtatggatggagtatatttatctgataaaatattatttgtagtcttgcctagggaaaggtggatgaacttgtacagtgcaaagtgaatagaatgtaaaattttctctcatcatatgcag

upper sequence: AT1G19270.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 5'ss of exon 7
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggtttt-----cttctcctctaatatgtccccaaacatacatcatctac--tcaaaagtgaaaacattttttagccggtaat-tgacaacttagctatactttgtag
|||||||||||||||||| ||||||||||||||||||||||| || |||||||| || || ||    || || ||||| || || ||||| |||||||||||  || |       || |    |  ||  ||   ||| ||      | ||   |       || || ||   | |   |||||  | | || || | ||   | || ||
TCTTATTGAATATAGGGCGCATCCTTTTTGGGTTCAGAAGTACTGCCCTTCTCATGAGCATGACAGAACACCTAGATGCTGTAGCTGTGAGAGAATGGAGgttagtctgaatgatttatttattcttaaatctgaaaatatggcctgtttatgattcttgaggagaatatagatgactgggtaacataaaaattttgttaatatatgcag

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|116457268|gb|EG499860.1|EG499860
EST:     CTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAG                         CCACGGAATACGAGATATGTTGAACTTAACGATGGACGGAAACTTTGCCTT
genomic: CTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttc ... tactttgtagCCACGGAATACGAGATATGTTGAACTTAACGATGGACGGAAACTTTGCCTT
EST: gi|86057437|gb|DR353194.1|DR353194
EST:     CTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAATNATGGAN                         CCACNNNANACGAGATATGTTGAACTTAACGATGGACGGAAACTTTGCCTT
genomic: CTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttc ... tactttgtagCCACGGAATACGAGATATGTTGAACTTAACGATGGACGGAAACTTTGCCTT
EST: gi|116457269|gb|EG499861.1|EG499861
EST:     TCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAAGAATGGAG                         CCACGGAATACGAGATATGTTGAACTTAACGATGGACGGAAACTTTGCCTT
genomic: TCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTG-AAAGAATGGAGgtgggttttc ... tactttgtagCCACGGAATACGAGATATGTTGAACTTAACGATGGACGGAAACTTTGCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTTGCAGTTGTGAAAGAATGGAGgtgggttttcttctcctctaatatgtccccaaacatacatcatctactcaaaagtgaaaacattttttagccggtaattgacaacttagctatactttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA