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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctggtcttctgaaaccttggtgtttaaccaatatctgtgctttttactttctacactgtatggaggatctaagagtataatctgatcctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC

Basic information

species Arabidopsis thaliana
transcript AT1G79000.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------gtaagtcctggtcttctgaaaccttggtgtttaaccaatatctgtgctttttactttctacactgtatggaggatctaagagtataatctgatcctttt---tatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
                                               |     || ||| |    ||| ||   ||      | ||||   ||     |  ||| |  |  |   |||     |    || ||||||| ||   ||   || |||| || || || |||||||| ||  |||| || ||||| || || ||||||||||||||||| ||  ||||||| || ||||| ||||||||||| ||||
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttggggggaccatatgactggaaactgtttttttta--gctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------gtaagtcctggtcttc-tgaaaccttggtgtttaacca-atatctgtg--ctttttactttctacactgtatggaggatctaa---gagtataatctgatc---ctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
                                               |     || ||| ||  | ||| ||   |     |||| | | | |    | ||||   |||| |  | ||   || || |     | || |||||||  |   |  | || |||| || || || |||||||| ||| |||| || ||||| || || |||||||||||||| || ||  ||||||| || ||||| ||||||||||| ||||
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 10
-----------------------------------------gtaagtcctggtcttctgaaacc--ttggtg--tttaaccaatatctgtgctttttactt--------tctacactgtatggaggatctaagagtat--aatctgatcctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
                                          ||       | ||| || ||||  ||| ||   | |  |||  ||||   | ||| |||        ||||  || |||  |   |  |  ||| |    | ||||  | ||| ||||| || ||||| || || ||||||   |||||||| || ||||||||||||||||| ||||| ||  | ||||| || |||||||| |||||||||||||
gtaacctttagttctaattccttgtccttgtgttgggtggaatattatacagccttgtggaaccctttgttggagtcattcaagttctgatttgtttccttcctgtagttctattctatataaatagttgagtagttttcgttatgattttcttt-tagATTGGATACCTTGAGTATTGCAAGAAACGTGGTTTTACAAGCTGCTACATATGGGCATGTCCTCCATTAAAGGGTGAAGATTATATTTTATATTGTCATC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
gtaagtcctggtcttctga---aaccttggtgtttaacc-----aatatctgtgcttt---ttactttctacactgtatggaggatctaagagtataatctgatcctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
|||| |   |    |  ||     | |||| |     ||      ||||    | | |   ||||| ||| | |||||      || | |   ||| |  |  | |||||||  ||| || || || ||||| ||||||   |||||||| || |||||||| || ||||||||||| ||  | ||||| || |||||||| |||||||| ||||
gtaaatttggacactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttc-ctgtaaattatatttga---tatgaattatttcttttta--gATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S462_17V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagtcctggtcttctgaaaccttggtgtttaaccaatatctgtgctttt-tactttctacactgtatggaggatctaagagtataatctgatccttt-ttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
   | |  |  | ||||  |       |||    |   | | | || | ||    | | |  ||||    ||  |  | |   | |   |  ||  | | ||  |||||||||| ||||| |||||   |  | | ||||| |  ||||| ||||| |||||||| || || || ||||| ||||||||||| |||||||||||||
---aatttt--ttttctttacttaaaatgtagtgctgctgtttctgttgttacgttgtttgtactg-gcagaccagttgaacttgttggcgtatgatctgttgcagATCGGCTATCTAGATTACTGTCGGAGGAGAGGTTTTAGTAGCTGTTACATTTGGGCTTGCCCACCTCTAAAGGGAGAGGATTATATTTTATATTGTCATC

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|116421535|gb|EG464127.1|EG464127
EST:     GATCTTATAACGGAGAAGCTCTGCGTACTTTTGTTTACCACGAAATTCTG                         ATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATA
genomic: GATCTTATAACGGAGAAGCTCTGCGTACTTTTGTTTACCACGAAATTCTGgtaagtcctg ... ctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATA
EST: gi|116455250|gb|EG497842.1|EG497842
EST:     GATCTTATAACGGAGAAGCTCTGCGTACTTTTGTTTACCACGAAATTCTG                         ATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATA
genomic: GATCTTATAACGGAGAAGCTCTGCGTACTTTTGTTTACCACGAAATTCTGgtaagtcctg ... ctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATA
EST: gi|116418401|gb|EG460993.1|EG460993
EST:     GATCTTATAACGGAGAAGCTCTGCGTACTTTTGTTTACCACGAAATTCTG                         ATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTAC
genomic: GATCTTATAACGGAGAAGCTCTGCGTACTTTTGTTTACCACGAAATTCTGgtaagtcctg ... ctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTAC
EST: gi|116447332|gb|EG489924.1|EG489924
EST:     GATCTTATAACGGAGAAGCTCTGCGTACTTT-GTT-AC-ACGAAATTCTG                         ATCAGCTAC-TAGA-TACTGCAAGTTGCGTG-TTTCACGAGCTGCTACATA
genomic: GATCTTATAACGGAGAAGCTCTGCGTACTTTTGTTTACCACGAAATTCTGgtaagtcctg ... ctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactttctacactgtatggaggatctaagagtataatctgatcctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
                                     atctgat  putative branch site (score: 4)
                                           tcctttttat  CT-rich tract
                                              tttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctggtcttctgaaaccttggtgtttaaccaatatctgtgctttttactttctacactgtatggaggatctaagagtataatctgatcctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT