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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG

Basic information

species Arabidopsis thaliana
transcript AT4G35950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 4
actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgt-----cagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
     | |  || |    | | || || |    |  | |        | || ||      |   | |||   ||   | | | || ||| || |||      ||||||||||||||||||| ||||||||  | ||||||||||||||||| ||||| ||||||| ||||
-----aaattaaattccaatcattctacagataatatccccttcgacctgtaaagatccaactgtagcccacttacatttttcacattgtttattgcactggcagATCTTCGAGATGACAAGCAGTTTTTTGTGGACCATCCTGGTGCTGTTCCTATCACCACTGCTCAG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
actgtatagcaagtg-tatacctt-tataaaag---acacttgca--agatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
       | | ||||  ||| ||| || | ||    || | |  |  | | | ||||    ||       |   | | | |  |       |     ||  || ||||||||||||||||||| ||||| ||  | ||||||||||||||||| ||||| || |||| ||||
-------aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 4
-----actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggtt--gttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
        | | | || |||  |      |       ||     ||   ||   ||     || | | |    | || |  ||    ||      ||   ||| ||||||||||||| ||||| ||||| ||  | ||||||||||||||||||||||| || |||| ||||
aactagtggcacaacatgtgcgtgaacccacgggtagcat----aaagcctcaggttg---caagctgcacatccttatattttcacaatgcacatttcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
-actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
   |||  |  |  |   |  | |    | | ||  |  | |  | |||  |||| | | ||    |   |||   ||| | | |  |||      | |||| ||||||||||| || ||||| ||||| ||||||||||||||||| || |||||||| ||||||
ttttgttaaaaatattcttggcctctacacatactatcaccaattgttctttcaattaa-gagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 5
-----actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
     |  ||      ||| | |    || | ||    |  |  | ||| |||   ||||  |   ||    |||| ||  ||||   |  |    ||   | ||| ||||| ||||| || ||||| | |||||||||||||||||| || ||||||||||| | ||||
gacagatggttgttttagtttctcaacttgtgaatattatattgatgattttcg--caaccaagagtctattccttattatttgt--gatttgtaatgagat-agACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 4
actgtat-agcaagtgtat--acctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
| | | | |  || | | |  |||| || | |    | |  | |  | |||  |||  | | ||      |||||    || | | |  |    ||  | |||| ||||||||||| || ||||| ||| | || ||||||||||| || || |||||||||||||| 
attttgttaaaaaatttctcaacctctacatatttta-tcaccaattgttctttcagttaa-gagttaatcctttaccgtttttttatttgaaatga-gacagACCTTCGAGATGATAAGCAGTTCTTCGTAGATCATCCTGGTGCCGTACCCATTACCACTGTTCAA

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
---actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
   | |   ||| | |  | | |  |   |  ||    ||  | | | ||  |  || | |  |   |    | | ||||| |  ||  ||  |||  |  ||||||||| || ||||| ||||| ||||| ||||||||||||||||| || ||  |  | | ||||
ctaaattagtagaaggaatttgcagtaggagtaggttatt-tatggttttgtgataattaacaaattttttttgtctgatt-ttcaatgttaattga-gctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG

upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------actgtatagcaagtgtatacctt-tataaaagacac----ttgcaagatcttc---agtcaactcatga----tcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
                                                      | || | ||  | | |    |  || |    | |    |||||| || ||    ||||       ||    | ||     |    ||| |  |||   |  ||  | ||||||||||||||||||| || ||||||  |||||||||||| || |  || || || ||    || 
gttcgtatttttctggctgcactgatcgttctgacgtacgctggactggtgtcgtttacaacagttatttgtagtacatgacgcccgcaactttgcaatatgttttggagtctgtctgagaagatttcttcgtctcacaattctgcaactgcgaatg--ggcagATCTTCGAGATGACAAGCAATTTTTCGCCGACCATCCTGGAGCGGCTCCGATCACAACCTCCCAA

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|124940404|gb|EL016858.1|EL016858
EST:     GAAGCACTATGCTCCTGGTGTCCCAATTGTCCTTGTTGGAACCAAACTAG                         ATCTTCGAGATGACAAACAGTTTTTCATCGACCA
genomic: GAAGCACTATGCTCCTGGTGTCCCAATTGTCCTTGTTGGAACCAAACTAGgttacttcct ... ttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCA
EST: gi|164149492|gb|ES084486.1|ES084486
EST:     ATTGTCCTTGTTGGAACCAAACTAG                         ATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTA
genomic: ATTGTCCTTGTTGGAACCAAACTAGgttacttcct ... ttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG
                                 gtctaac  putative branch site (score: 2)
                        tttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG

- - - - - - - - - - - - - -aaagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - aactcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctaacc