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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacgcacactgttcgctctatgctttggaggtgattttcatccagtctagttatgctacacaattgtttaaacacaattttaatcttagctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA

Basic information

species Zea mays
transcript GRMZM2G090156_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090156_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g02880.1 (Oryza sativa), 3'ss of exon 1
gcacg-cacactgttcgctctatgctttggaggtgattttcatccagtctagttatgctacacaattgtttaaacacaattttaatc-ttagctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA
|| |   |   | || |||   ||   || |  || |||     || | |  ||||   |   |||  | | ||||  |  ||  ||  || |||| || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| ||||| |||||||| |||||||||||||| ||||| || || |||||||||
gctcaatatgttattggctaagtgtcatgcatatggtttgtgatcaatatc-ttatttaatctaat-atatgaacatgacatttgtcgctaactaccgtcagGTGGATTCCGGATGGACAGCTGTGCCCTACTGTGCCAAACAGATCCAATTACATCCACTGGATTGAGGATCTTCTCTCATCAGACCTCATACCACCAATA

upper sequence: GRMZM2G090156_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G26370.1 (Glycine max), 3'ss of exon 1
gcacgcacactgttcgctctatgctttggaggtgattttcatccagtctagttatgctacacaattgtttaaacacaatt-ttaatcttagctactgt-tagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA
   | |    | | |  | |    |    || ||   ||  |       |  | || || | |||| |  |  ||  |||  | ||   |   | | | |||||||||||| |||||||| ||||| || ||||| || ||||||| |||||||||||| ||| |  |  |||||||||| ||| |  | || | |   |  
--ccactttttatccatttttccttgcaaagctgtaatttttatgccaaacctgtgttataaaattttccacccaagattactgatggaatgcattttgtagGTGGATTCCTGATGGACACCTCTGTCCAACTGTGCCCAACAGGTGCAACTACATTCATTGGCTTCAACATCTTCTCTCATCAAACATCATTCGAAACACC

upper sequence: GRMZM2G090156_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G09280.1 (Glycine max), 3'ss of exon 1
--gcacgcacac-tgttcgctctatgctttggaggtgattttcatccagtctagttatgctacacaattgtttaaacac-aattttaatcttagctactgt-tagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA
    | |  ||| |   ||||  |   |    ||    |||| ||||  | |   | ||| |   |    |||  |  | ||   |  |   |  |  | | |||||||||||| |||||| | ||||| || ||||| |||||||||| ||| |||||||| ||| |  |  | |||||||| || ||  | || |||   |  
gcctatgggcacatacccgcttcagaat----agccactttttatcccattttcct-tgcaaagtagcaatttttatgccaaacctgttggaatgtgttttgtagGTGGATTCCTGATGGAAACCTCTGTCCAACTGTGCCAAACAGGTGCAATTACATTCATTGGCTTCAACACCTTCTCTCATCTGACATCATTCCAAACACC

upper sequence: GRMZM2G090156_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G21070.2 (Arabidopsis thaliana), 3'ss of exon 1
gcacgcacactgttcgctctatgctttggaggtgattttcatccagtctagttatgctacacaattgtttaaacacaattttaatcttagctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA
        |   ||     | | |   |||  |   |||  | |  || ||         ||| ||  |||   || |    | |||||  ||    |||||||||||| ||||||||||| ||||| |||||||| || || || || |||||||| |||||| | |||||| | ||||| |   | || | |    | 
------gtatgatttcaattgtacaaaggaactagcttttttgctctcaaga--------acagttagttatttacca---aagtctta--tatatatagGTGGATTCCTGATGGACAGCTTTGCCCAACTGTTCCTAATAGATCGAATTACATTCATTGGATCAATGATCTTTTGTCCTCTGGGATCATTCAAAGTTTG

upper sequence: GRMZM2G090156_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv03s0038g02100.t01 (Vitis vinifera), 3'ss of exon 1
gcacgc-acactgttcgctctatgctttggaggtgattttcatccagtctagttatgctacacaattgtt-taaacacaattttaatcttagctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA
   ||| |  || || |   ||    ||      | |     |   || |   |  | ||     ||||  |  |   | |   ||| | || |      ||||||||||| ||||| ||||| ||||| || ||||||||||| || ||||| || || ||||| || |||||||| || || ||  | || ||    | |
attcgccaagctttttgtcatagaaatttccaaagttcaggcttatgtgttaatgggatatgtgtttgtggttgatttagtgaaaatatgagttgt--gcagGTGGATTCCTGATGGGCAGCTTTGCCCTACAGTTCCAAACAGATCAAACTATATCCATTGGATTGAAGATCTTCTGTCTTCTGACATTATTCCTAAGACA

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|71430690|gb|DR811740.1|DR811740
EST:     ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTG                         GTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
genomic: ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
EST: gi|60398656|gb|DN231472.1|DN231472
EST:     ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTG                         GTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
genomic: ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
EST: gi|74236801|gb|DT644715.1|DT644715
EST:     ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTG                         GTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
genomic: ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
EST: gi|76293395|gb|DV032963.1|DV032963
EST:     ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTG                         GTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
genomic: ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
EST: gi|71443732|gb|DR824782.1|DR824782
EST:     ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTG                         GTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
genomic: ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
EST: gi|71444538|gb|DR825588.1|DR825588
EST:     ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTG                         GTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
genomic: ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
EST: gi|76019740|gb|DT946910.1|DT946910
EST:     ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTG                         GTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA
genomic: ACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

CCGTCTCCGGCAGCGGGCGCGCGTCCGTTGATTTCACCGACTTCTCCTCCACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

CCGTCTCCGGCAGCGGGCGCGCGTCCGTTGATTTCACCGACTTCTCCTCCACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

CCGTCTCCGGCAGCGGGCGCGCGTCCGTTGATTTCACCGACTTCTCCTCCACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 83

CCGTCTCCGGCAGCGGGCGCGCGTCCGTTGATTTCACCGACTTCTCCTCCACCAGGGAGCTCACGCGCGTGCTCCTCCTCCACGACCATGGCGTCAACTGgttggtgtca ... ctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctagttatgctacacaattgtttaaacacaattttaatcttagctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA
                                 ttttaat  putative branch site (score: 83)
                 aattgtttaaacacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacgcacactgttcgctctatgctttggaggtgattttcatccagtctagttatgctacacaattgtttaaacacaattttaatcttagctactgttagGTGGATTCCAGATGGACAGCTCTGCCCGACTGTTCCAAACAGGTCCAACTACATTCACTGGATCGAGGATCTTCTCTCCTCAGATCTGATCCCACCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
gcacgca
- - - - - - - - - -tatgctt
- - - - - - - - - - - - - - - - - - - -catccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gctacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaca