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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G32790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------gtgagattttcctcta-------ctatgcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtc-tatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                             | |  | ||  |  |        ||||||||       |    |   | || |            | ||||||    ||||| | || ||||||||||||||||||||||| ||||| ||||| || ||||| |||||||||
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G044246_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG---------------------------------
                                  | || |  |     | | | ||   | | |      | |   || || ||  || |  | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||||||||||||||                                 
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                  | || |  |     | | | ||   | | |      | |   || || ||  || |  | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||||||||||||||
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatt-tagtcttgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                  | || |  |     | | | ||   | | |      | |   || || ||  || || |  |  ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G069102_T03 (Zea mays), 3'ss of exon 4
-----------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatt-tagtcttgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                        | || |  |     | | | ||   | | |      | |   || || ||  || || |  |  ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
cttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G454261_T01 (Zea mays), 3'ss of exon 1
----------------------gtgagattttcctctactatgcaaagtttctgatggttagc--gactgaggaaaatgatttagtcttgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                       ||   |||    ||   || | ||| || || ||   | |     | |   | ||  ||   |  ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
acatactattgctaccctgtttctgctgtttcaaactgagatactaaggttgtgttgccaatcctacataacatatatacttattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                  | || |  |     | | | ||   | | |      | |   || || ||  || |  | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G457231_T01 (Zea mays), 3'ss of exon 7
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG---------------------------------
                                  | || |  |     | | | ||   | | |      | |   || || ||| || |  | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||                                 
gtatgcaaaccttccagaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatttgatatggtctctaagaaaattggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
-------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                          |   |   |  |  | | |||  | | ||||||   | |   || || ||  || |  | | | ||| || || || |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgata--tggtctctaagaaagttggtcgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 6
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                  | || |  |     | | | ||   | | |      | |   || || ||  || |  | | | ||| || | ||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| ||||||| |
gtatgcaaatcttctagaaccaacatgcatgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctccagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGATG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 3
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                  | || |  |     | | | ||   | | |      | |   || || ||  || |  | | | ||| || | ||| |||| ||||| ||||| ||||||||||| || |||||||| || ||||| |||||||||
gtatgcaaaccttctggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctccagCCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G376619_T01 (Zea mays), 3'ss of exon 6
gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                       |   || || ||  ||    | | | ||| || || || |||| ||||| ||||| ||||||||||| ||||||||||  || ||||| |||||||||
---------------------------------------gtatctaagaaagttggccgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTACACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G398795_T01 (Zea mays), 3'ss of exon 7
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                                  | || |  |     | | | ||   | | |      | |   || || ||  || |  | | | ||| || | ||| || | ||||| | ||| ||||||||||| ||||||||||| || ||||| |||||||||
gtatgcaaaccttctggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctacagTCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G324221_T03 (Zea mays), 3'ss of exon 6
-----------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                        | || |  |     | | | ||   | | |      | |   || || ||  || || | | | ||| || ||||| |||| |||||  |||| |||||||| || ||||||||||| || ||||| |||||||||
cttccgaaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtttctaagaaagttggttgattttctgtgctctgcagTCTGACGATGAATGTGAAATGTGTGCTAGGACTATCTACTGCACAAACATTGACAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
------------------------gtgagattttcctctactatgcaaagt----ttctgatg--gttagcgactgaggaaaatgat-ttagtcttgtcta-tgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                        ||     ||| |   | | || ||| |    || || ||  |||     |  |  || ||||| || ||  | |  | | |||| ||||||||| || ||||||||||||||||| || |||||||| || || || ||||||
gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------gtgagattttcctctactatgcaa-agtttctga---tggttag--cgactgaggaaaatgatttagt--cttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
                 |  |   ||     |  ||||| | ||||  |||    || | |   || |   |    | | |||||  ||   |  | ||| |||||||||||||||| ||||||||| | || ||||||||||| || || |||||||||
ggaattgtttcatacttgcaacgattgttagtgatatgccatagttcttgaatacggctcggatgaattctggctctaacttagttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG

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|86081011|gb|DR376768.1|DR376768
EST:     TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGG                         ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
genomic: TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGGgtgagatttt ... gtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
EST: gi|86051671|gb|DR347426.1|DR347426
EST:     TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGG                         ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
genomic: TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGGgtgagatttt ... gtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
EST: gi|86051676|gb|DR347431.1|DR347431
EST:     TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGG                         ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
genomic: TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGGgtgagatttt ... gtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
       ttctgat  putative branch site (score: 3)
                                         tcttgtct  putative PPT
                             aaaatgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG