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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctcccccgccccgcccccttctctcctctgcctttacgattgtattttaattccgaacatcttgttttgcctctgcctggctgcctgccttccttcctgacaccacccctggcccctgcgttcccgcaaaacttttcag

Basic information

species Zea mays
transcript GRMZM2G114126_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 9
CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctcccccgccccgcccccttctctcctctgcctttacgattgtattttaattccgaacatcttgttttgcctctgcctggctgcctgccttccttcctgacaccacccctggcccctgcgttcccgcaaaacttttcag
|||| || |||||||| |||||||| || |||||  ||||||| ||||||||||||||||||||||| |||||||| || || || |||||||||||||||||  | |||       ||    ||| |  |  | |   | |   |||  |      |  | | ||||   || |         |   | | ||    | |||                                           
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctcattttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttcatttcgtggaaactttcag-----------------------------------------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 9
CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctcccccgccccgcccccttctctcctctgcctttacgattgtattttaattccgaacatcttgttttgcctctgcctggctgcctgccttccttcctgacaccacccctggcccctgcgttcccgcaaaacttttcag
| || ||||  ||| |||||||||| ||||| || ||  | || ||||||||||| ||||||| ||||||  |||| || |||||  |||||||||||||||  |||  ||        |  ||       ||  ||     |  | | ||    |       | |     |    |   || |    ||  |  | | |                                              
CTGCCCCTAGAAAGTTGTTGGCATCAGATTCTCGACTACGCCCAGATAGATATGCACTCGAGATGGGCGATCTGTCAAAATCTGGGACAGAAAAGAGCAGgttactcaccctttcttttgttcctcctatccccttgtgcccaaaaatttagcagagcattttagaagcactaacacgaatgtcaaattgagtaacgtac----------------------------------------------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 9
CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctcccccgccccgcccccttctctcctctgcctttacgattgtattttaattccgaacatcttgttttgcctctgcctggctgcctgccttccttcctgacaccacccctggcccctgcgttcccgcaaaacttttcag
| || ||||| ||| ||||||| || ||||| || ||  | || ||||||||||| ||||||| ||||||  |||| || |||||  |||||||||||||||  ||   ||        |   |       ||  ||     |  | | ||   ||       | |     |  | |   ||      ||  |  |   |                                              
CTGCCCCTAAAAAGTTGTTGGCGTCAGATTCTCGTCTACGCCCAGATAGATATGCACTCGAGATGGGCGATCTGTCAAAATCTGGGGCAGAAAAGAGCAGgttactgaccctttcttttgtttctcctgtccccttgtgcccaaaaatttagcatagcattttagaagcactaatactaatgtaaaattgagtaacagac----------------------------------------------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G09300.1 (Arabidopsis thaliana), 5'ss of exon 9
CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctcccccgccccgcccccttctctcctctgcctttacgattgtattttaattccgaacatcttgttttgcctctgcctggctgcctgccttccttcctgacaccacccctggcccctgcgttcccgcaaaacttttcag
| || || || ||||||||| | |||||||| ||| |  | || |||||||| || || |||| ||||||||||||||| || ||||  || ||||||||||||               ||       | ||||  |  | |   |||| | |  ||      | ||   | |||  ||         | | |  | || |   ||| |  |                                  
CTGCCCCGAAAAAGCTGTTGCCCTCTGATTCACGGTTACGACCTGATAGATACGCACTTGAGATGGGCGACATGTCCAAATCAGGCTATGAGAAGAGCAGgtatggta-----------gcaaaaacttgtccttaggatctgaaattgaagtaaaagctaataaattgggatttttct-------aattcttctcctcatctttgatatgaag--------------------------------

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|149105112|gb|EE290595.2|EE290595
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|74236528|gb|DT644442.1|DT644442
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGTTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|60356147|gb|DN223120.1|DN223120
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|67022184|gb|CO450933.1|CO450933
EST:     TATGCCCTCGAGAAAGGCGACATGTCCAAGTCTGGCTCANAAAAGAGCAC                         GCTGGAGGAGCACCANAGAGCCGAGAAAAGGACTCCAGAAGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|78120438|gb|DV538822.1|DV538822
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|60396557|gb|DN229426.1|DN229426
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|67032806|gb|CO461555.1|CO461555
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCANGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|71329768|gb|DR801597.1|DR801597
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|71759542|gb|DR957479.1|DR957479
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
EST: gi|14243772|gb|BG841435.2|BG841435
EST:     TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAG                         GCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGA

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: 49 (upstream exon), 47 (downstream exon)
Score: 99

CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGAGCAGTTCACTCCGCGATGGTTCAACGTGACGGATGCGGTCGCCTCCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 396

CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGAGCAGTTCACTCCGCGATGGTTCAACGTGACGGATGCGGTCGCCTCCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 331

CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGAGCAGTTCACTCCGCGATGGTTCAACGTGACGGATGCGGTCGCCTCCACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 136

CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctc ... aacttttcagGCTGGAGGAGCAGCAGAGAGCCGAGAAAAGGACTCGAGAGGCCAAGGGCGAGCAGTTCACTCCGCGATGGTTCAACGTGACGGATGCGGTCGCCTCCACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCACCTAAGAAGCTGTTGGCATCTGATTCCCGGCTGAGGCCCGATAGATATGCCCTCGAGAAGGGCGACATGTCCAAGTCTGGCTCAGAAAAGAGCAGgtatctcctcccccgccccgcccccttctctcctctgcctttacgattgtattttaattccgaacatcttgttttgcctctgcctggctgcctgccttccttcctgacaccacccctggcccctgcgttcccgcaaaacttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG