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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA

Basic information

species Arabidopsis thaliana
transcript AT5G37510.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 1
gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgat-tggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
| ||||  |||    |||  | ||  |||   ||   | || | ||  |||| || | || | || |    ||| ||  |    |||    |  || |||||| ||||||||||||||||||  | || ||  |||| ||||| || |||||||| || ||||||||  ||||||||||||| ||  |||| || || || |||||
gctagt--gatagttggactaattgaatg---attagtagagtgtgtgcgtttatctagtaggatttgca-ggagttcttaacgttggagcgccttgttgtaatagGGATGAAGATTAAGACAAACACGCCAGTAGCAAAGAAAGCCAGGGAGGGTGTCATGGAGTTCCTGTTGATGAATCATCCGCTGGACTGCCCAATCTGTGA

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 1
gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgt---aacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
       | || |||   ||| ||   ||  ||    | |||        |||||       |  || |    ||||| ||  |   | |   || |||    |  ||||||||| || |||||  | || ||  | || ||||||||||||||||| || |||||||| ||| ||||||| || ||  |||| || || || |||||
-------ccataccattcaaaattggttggaga-aactagatacctcaaattgatgtacctgaattagtgaattttggagcactgaatgatcattcttgctgaattagGGATGAAAATCAAGACAAACACCCCAGTGGCGAAGAAGGCGAGGGAGGGTGTCATGGAGTTCTTGCTGATGAACCATCCACTGGACTGCCCAATCTGTGA

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA-
     |  |  |||  | |   || | | || |||   |  |||| | |  | |||| |   ||   | |  |    ||  | |    |   | |  | |   ||||||||| ||||||||||| |||||  | || |||||||| || || ||||||||||||||||| ||||||||||| || || ||||| || |||||||| 
acagataagcatccttgga---ttttgttctaatgaggt--ttttaaccagttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctt-taggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 1
-gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
      |  |  |||  | |   || | |  | |||   |  |||| | |  |  ||| |   ||   | |  |    ||  | |    |   | |  | |   ||||||||| ||||||||||| |||||  | || ||||||||  | || ||||||||||||||||| ||||||||||| || || ||||| || ||||||||
aacagataagcatccttgga---ttttgttttaatgaggt--ttttaaccagttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctt-tagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
-------gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
       | |  |  |  | ||| |  || |   |  |  ||| |||  ||   |  ||||||| ||  | ||||| || |||  |  | ||        ||||| |   ||||||||||||||||||   ||||||  | || || ||||| || || ||||| ||||||||| || |||||||||| |||||||||||||| ||||||||
ttggctagatgatctgtatgcagcactatgttattcattctggcttggattatttttttgattgttg--acatattagggtttttttttttt--------ttttttt--tagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S28_321V6.2 (Physcomitrella patens), 3'ss of exon 1
gttagttcgattccaggaaaat--------ttctatgctgatggattg-----attttg------atcgttgattggtggaatatatt-----tgg-atttggtgctattgctaagagtttttgtaa----cagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
    ||||||||||  |||| |        || | || || |     |     ||| ||      ||   || ||||| ||||  |||     ||| |   |  |    |||||||||     |       |||| ||||| || ||||| || |||||  | |||||||| || ||||||||||||||||||||  |  ||||||| ||||| || |||||||| ||||| ||
----gttcgattccgcgaaactagaagctgttttttgttggtttcccgcaaacattgtgtggaggatttctggttggtagaatggattgtgtgtggcaaaagaagggggtgctaagaggcggagcggattccagGTATGAAAATCAAGACGGACACACCTCTGGCTAAGAAAGCAAGGGAGGGAGTGATGGAGTTCCTTCTGATGAACCACCCCTTAGATTGTCCGATTTGCGA

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S170_67V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------gttagttcgattccaggaaaatttctatgctgatggattgattttgatcg-ttgattggtggaatatatttggatttggtgctattgctaagagtttttgta-acagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
                           ||   ||  || || |    ||   || |   | |   | || | ||   |||    |||    | |   ||||     |   | |    |     |||   | ||| ||||| |||||||| | ||||||  | |||||||| || |||||||||||||||||||||||||||||||| || || |||||||| || ||||| ||
gtctgattccattagttagtaaccctcttttctcagttgcaagctgtttgacatacaattcgtgcggttcttataacttggggtgtgtctaaaagcgggatactaagaggtcgaatggctgaattgcgtatagGTATGAAAATTAAGACCGGTACACCTCTGGCTAAGAAAGCAAGGGAGGGAGTGATGGAGTTTTTGTTGATGAACCATCCATTGGATTGCCCGATTTGCGA

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|116457684|gb|EG500276.1|EG500276
EST:     TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTG                         GGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
genomic: TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcga ... tttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
EST: gi|116446464|gb|EG489056.1|EG489056
EST:     TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTG                         GGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
genomic: TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcga ... tttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
EST: gi|116457686|gb|EG500278.1|EG500278
EST:     TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTG                         GGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
genomic: TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcga ... tttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
EST: gi|116424612|gb|EG467204.1|EG467204
EST:     TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTG                         GGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
genomic: TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcga ... tttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
EST: gi|125050274|gb|EL122543.1|EL122543
EST:     AAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTG                         GGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
genomic: AAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcga ... tttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
EST: gi|116411626|gb|EG454218.1|EG454218
EST:     TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTG                         GGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
genomic: TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcga ... tttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAG
EST: gi|125197834|gb|EL212788.1|EL212788
EST:     TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTG                         GGATGAAGATTAAGA
genomic: TGAGAAATCTCCTAAGCCTGTAGCTTCATGTGCCATGCCTGCGCTTCCTGgttagttcga ... tttgtaacagGGATGAAGATTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
 cgttgat  putative branch site (score: 5)
                                           tttttgt  putative PPT
           aatatatttggattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA