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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgtctgtgtgataaaacgagtacttgtttaaagacaacgtgaaaccctgatggattataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA

Basic information

species Arabidopsis thaliana
transcript AT4G31990.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 7
tactgtctgtgtgataa----aacgagtacttgtttaaagacaacgtgaaaccctgatggattataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA
   ||||||| |  ||     ||     | || | |    || |     ||     |||  ||  | |  |   |  |||  |  || | |||       | |||  || ||||| ||||| ||  |  |||| || || || |||||||||||||||||||| |||||||| || ||||| ||||  |||||||| |||||||
-cttgtctgtttactattgttaattgtcaattttctgtttactattgttaatttctatgtgttg-agtattggtttgtga--tattgatttgtgtgtccaatagGCTGCCCCAGATGGATCTTTTGTTCTGCTGCATGGTTGCGCTCACAACCCAACTGGAATAGACCCAACTCCGGAACAATGGGAGAAAATTGCAGATGTCA

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 7
-tactgtctgtgtg-ataaaacgagtacttgtttaaagacaacgtgaaaccct-gatggattataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA
 | |||  | | |  ||| |     |   |  | |||   |||     ||  |  || |||| |    |  | | |  | |   | || | | | |   |||||  ||||| ||||| || ||  |  |||| || || ||||||||||||||||||||||| |||||||| || ||||||||||  |||||||| |||||||
gtcctgaatttatctatagagtttttttgttctgaaaatgaacacttcactttcaattgattgtttatgccattatctattcatttttttttcaca---acagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 7
tactgtctgtgtgataaaacgagtactt-----gtttaaagacaacgtgaaaccctgatggatt---ataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA
       |   |   || | || | ||       |||||||    | | || ||   ||  | |   | ||||  ||||  |  ||||||    | |      | |||  |||||| |||||||| || ||||| ||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||| |||||| |||||||| |
--agacgtacataggaacatgaattctcatttgatttaaaggttccttcaatccaatataaaattgaacaatgcctaattgtacatttctacatttt------ttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAACCCTACTGGTATCGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATGTAA

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 7
---tactgtctgtgtgataaaacgagtacttgtttaaagacaacgtgaaaccctgatggatt---ataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA
   |||     |  | |||||        |  ||||||||   | | || |    ||  | |   | | ||  ||||  |  ||||||    | |      | |||  |||||| |||||||| || ||||| ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||||| |||||| |||||| | |
gcctacatatagaatcataaattttcatttaatttaaagattccttcaatctaatataaaattgaacagtgcctaattgtacatttctacatttt------ttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCTACTGGTATTGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATTTAA

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 9
tactgtctgtgtgataaaacgagtacttgtttaaagacaacgtgaaaccctga--tggattataatggttaatctt-gaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA
        || || |    |  |   |||||| || | ||  |  |   |     |  |||    |  |||||    ||   | | ||   |    | | |||| ||| ||||||||||| ||  | |||||||| || |||||||||||||||||||| ||||| ||||| || |||||||||| ||| |||||||||||||
---caaaagtttgttcttgcttggtattgtttcaatataattttcatttccaggctaaattcacttctttaattcaagagagtttatttatttttgtttccagGCAGCCCCAGAAGGATCTTTTGTGTTGCTTCATGGCTGTGCTCACAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCA

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 7
-------------tactgtctgtgtgataaaacgagtacttgtt-taaa---gacaacgtgaaaccctgatggattataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA
             |    |||   |||    | | ||  |     || |   || | |    |         |  |    |  || |      | |   | | || ||| ||| ||| | || || || || ||  | || ||| | ||||| ||||| |||||||||||||| ||||||||||||||||| || ||||  || ||||||||| | |
gtagaagccaaacttagatcttaatgacgtcaagtgtgttcaccatatatttgatagcagcgatttacagcagtattcctttattgaggacacactatggctttg-aaattgtgcagAACGCACCTGAGGGTTCAATTATATTGTTGCACGGGTGTGCACACAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTA

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|124993183|gb|EL065452.1|EL065452
EST:     ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAG                         GAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGG
genomic: ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAGgtttgtttgt ... aaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGG
EST: gi|47828582|gb|CK118266.1|CK118266
EST:     ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAG                         GAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCA
genomic: ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAGgtttgtttgt ... aaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCA
EST: gi|124860684|gb|EH945121.1|EH945121
EST:     TACCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAG                         GAAGCTCCAGAAGGAT
genomic: T-CCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAGgtttgtttgt ... aaatgtacagGAAGCTCCAGAAGGAT
EST: gi|124979050|gb|EL052150.1|EL052150
EST:     AGCAGATAATAAAG                         GAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCC
genomic: AGCAGAT-ATAAAGgtttgtttgt ... aaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCC
EST: gi|124917880|gb|EH991754.1|EH991754
EST:     ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAG                         GAAGCTCCAGAAGG
genomic: ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAGgtttgtttgt ... aaatgtacagGAAGCTCCAGAAGG
EST: gi|125166187|gb|EL192105.1|EL192105
EST:     ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAG                         GAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTG
genomic: ATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGCAGATATAAAGgtttgtttgt ... aaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccctgatggattataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA
                   ggttaat  putative branch site (score: 4)
           attataatggttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgtctgtgtgataaaacgagtacttgtttaaagacaacgtgaaaccctgatggattataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT