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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctattatcaatcctttaatctttcttttttaattcagtactcgtcttggagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC

Basic information

species Arabidopsis thaliana
transcript AT1G13560.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g02750.4 (Oryza sativa), 3'ss of exon 6
gtatg-ctatt-atcaatcctttaatctttc-ttttttaattcagtactcgtcttg-gagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC
||| | ||||| | |||   ||    ||| | | |   |||  |       ||||| ||   |||| |     |||||     | |  ||||||| ||| |||| ||||||||||| ||||||||||||| || ||| |||||||  ||| | ||| | ||| | ||||||||  | || || |||||||
gtaaggctattcaccaacttttctcccttgcatgtcccaatatacggaaaatcttgtgaactgattgtatttattttat----atattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC

upper sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 6
gtatgctattatcaatcctttaatctttcttttttaattcagtactcgtcttggagtcgattatgaa--ggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC
      ||  | ||    |  |   ||| | ||| || |  | | |  | ||  ||||| || |||     ||||      | |  |||||||| || |||| ||||||||||| || ||||||||||  | ||| |||||||| ||| | ||||||||| | ||||||||    || || |||||||
-----gtaagaccacctgtcaatattttttatttcaagt--gcaatgattttcaagtcg-ttgtgagctcattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC

upper sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 7
gtatgctattatcaatcctttaatctttcttttttaattcagtactcgtcttggagtcgattatgaaggttttaccctaaaaa--cagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC
|||||    |   |   ||||   || |  ||||||| ||| |           || | || | ||   | ||     | |    |||||||||||  |||| ||||| ||||| || |||||||||||| ||||||||||||  ||| | || || || ||| |||||||||| || || ||||| |
gtatgtctcttatag--ctttgg-ctattatttttaaatcattg--------aaagacaataaagatactcttctgtgatattttcagTTTGAAGCATTGGCTTTTGGGAGCACAGCCATGTGTGGAAGAAATACTTTCTGGTGGTGGTTAATATCTGCAATTACATTTTATGGTGCAACCTGGGAGC

upper sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 7
gtatgctattatcaatcctttaatctttcttttttaattcagtactcgtcttggagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC
|||||    | |   | ||||     || ||||| |||     |       | ||| |  | ||  | | |  | | |     |||||||||||  |||| ||||| ||||| || ||||||||||||  |||||||||||  ||| | || || || ||| |||||||||| || || ||||| |
gtatgtc--tcttgttgctttggctattatttttaaatcattgaaagagaatagagacagtcatctatgat--aacttcttttcagTTTGAAGCATTGGCTTTTGGGAGCACAGCCATGTGTGGAAGAACTACTTTCTGGTGGTGGTTAATATCTGCAATTACATTTTATGGTGCAACCTGGGAGC

upper sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 7
gtatgctattatcaatcctttaatctttctttttta--attcagtactcgtcttggagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC
         |||  ||  |||  ||| |  || |||  ||  |||| | |        |    |   ||  || |    |     ||||||||| ||||||| ||||| |||||||| ||||||||||||  | |||||||||||||||| ||||||||| ||||||||||| | || ||||||||||
--------gtatgtatttttttgtctattgttgttattatggagtagtggcaactttattaccttaaaaacttatgttgtcttt-cagTTTGAAACCATGGCTTTTGGGAGCACTGCTATGTGTGGAAGAACTTCTTTCTGGTTCTGGGTAATTTCAGCTGTTCCATTTTATTGTGCAACATGGGAAC

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|86070080|gb|DR365837.1|DR365837
EST:     TGGTTGTGACGCGCTTGCTTGTGCG                         TTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC
genomic: TGGTTGTGACGCGCTTGCTTGTGCGgtatgctatt ... ctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC
EST: gi|86070077|gb|DR365834.1|DR365834
EST:     TGGTTGTGACGCGCTTGCTTGTGCG                         TTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC
genomic: TGGTTGTGACGCGCTTGCTTGTGCGgtatgctatt ... ctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC
EST: gi|164202941|gb|ES188864.1|ES188864
EST:     CGATCATGGTCGTGACGCGCTTGCTTGTGCG                         TTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC
genomic: CGATCATGGTTGTGACGCGCTTGCTTGTGCGgtatgctatt ... ctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC
EST: gi|86070081|gb|DR365838.1|DR365838
EST:     TGGTTGTGACGCGCTTGCTTGTGCG                         TTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC
genomic: TGGTTGTGACGCGCTTGCTTGTGCGgtatgctatt ... ctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaattcagtactcgtcttggagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC
                                           ccctaaa  putative branch site (score: 3)
                                      ttttaccct  CT-rich tract
                            attatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctattatcaatcctttaatctttcttttttaattcagtactcgtcttggagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT