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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaaaactagaagtacaagctgatgtgtgaatctgcataaaaaatagcatatgataagctctggcaaagcaactaacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA

Basic information

species Zea mays
transcript GRMZM2G132866_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 8
ttaaaaaactagaagtacaagctgatgtgtgaatc--tgcataaaaaatagcatatgataagctctggcaaagcaact------aacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA
      | ||||    |  |    || | ||| ||  |||||  | || ||   || |   ||| | |  ||   | |       ||      |||  || ||||||||||| || ||||||||| | || || |||||||||||||| ||||| || || |||||||||||||||||||||||| || | || ||
------agctagtctcatcaatgcatatttgattcattgcatgtagaa-agggcatcact-gctatagacaattgattctttatgacattggtgttttgcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA

upper sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G46230.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------------------ttaaaaaactagaagtacaagctgatgtgtgaatctgcataaaaaatagcatatgataagctctggcaaagcaact--------aacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA
                                                                                           ||   ||     ||  | |   |||  | |   | |  |||  || ||    |||||    | |    | | |  |        |  | || | |    |  || ||||||| || ||||| | |||    |  |||  ||  || ||  |  | ||||| ||||||||||||||||| |||||| ||||| ||||
gtattaatagttctaaagtttctgataatctcttactttattatgtatcaaggcatgagttttattgtaaacctcctgacactgtcttcgattcctaagtgtaaaaaaaagcatgagttttatgtttctatagtaagtaat-catgatgttgttttagtatgtactttttgtcttagtgtcatattctttcggtttcagCAACACTGGGACAAACTCTAGTTAGGCATCGATCAAAACCACGGATATACATTGGATGCATGAAATCTGGGCCTGTCCTATCCCAAAA

upper sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 7
---------------------ttaaaaaactagaagtacaagc-tgatgtgtgaatctgcataaaaaatagcatatgataagctctggcaaagcaac--------taacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA
                      |||     ||    || |||| |||  | |   | |  |||  ||||| |  |||||    | |    | | |          || |   | | |    |  || ||||||| || ||| | | |||    | ||||  ||  || ||  |  | ||||| ||||||||||||||||| |||||| ||||| ||||
gtattaatagtaaagtttctgataatctcttatgtataaaagcatgagttttatgtttctatagtaaataac-catgatgttgttttaatatgtactgtttgtcttagcattatattctttctgtttcagCAACACTGGGAGAAACTCTAGTTAGACATCGATCAAAACCACGGATATACATTGGATGCATGAAATCTGGGCCTGTCCTATCCCAAAA

upper sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 7
ttaaaaaactagaagtacaagctgatgtgtgaatctgcataaaaaatagcatatgataagctctggcaaagca-actaacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA
      ||    || |         | | |||||     |      |  ||| | | |   | || |   ||  |||   | ||  | |     | |||||| ||||| |||       |  | | | |     |||||||  |||||||||| || ||||||||||||||||||||  |  |  | ||
---gtgaatataaactctcttaaagtatctgaattgttttgtttcttgtcatctca-agtttgtgcctttgctcacttctgtcatggat--atttctgcagCCACGCTTGGAGCAGAATTAGCAAGATACCGGATGAAGCCCCGAGTGTACATTGGTTGCATGAAATCTGGACCTGTTCTTGCTCAGAA

upper sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 7
ttaaaaaactagaagtacaagc-tgatgtgtgaatctgcataaaaaatagcatatgataagctctggcaaagcaactaacgccaaagttcggcatt--tgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA
    |    ||    |  |||  | || ||||    || | |||  |  ||   || |    |    |    ||  |   |   |  ||   ||||  ||||||||| || |||   | | |  |||  ||    |  || || ||  | ||||| |||||||||||||||||||||||  || |  ||||
---gattcttactcttgaaagtatcatatgtggccatgtagaaatgaatgctattgcttcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA

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|211309888|gb|FL092753.1|FL092753
EST:     GGACGCCGACTTTTATGTTAAGGTTGACGATGATGTCCATGTGAACATAG                         CAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACA
genomic: GGACGCCGACTTTTATGTTAAGGTTGACGATGATGTCCATGTGAACATAGgtaatctccc ... gcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACA
EST: gi|33101737|gb|CF061697.1|CF061697
EST:     GGACGCCGACTTTTATGTTAAGGTTGAC---GATGTCCATGTGAACATAG                         CAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACA
genomic: GGACGCCGACTTTTATGTTAAGGTTGACGATGATGTCCATGTGAACATAGgtaatctccc ... gcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACA

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), 47 (downstream exon)
Score: 102

GCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACGATGATGTCCATGTGAACATAGgtaatctccc ... gcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

GCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACGATGATGTCCATGTGAACATAGgtaatctccc ... gcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 250

GCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACGATGATGTCCATGTGAACATAGgtaatctccc ... gcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 321

GCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACGATGATGTCCATGTGAACATAGgtaatctccc ... gcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcatatgataagctctggcaaagcaactaacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA
                           aactaac  putative branch site (score: 321)
     atatgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaaaactagaagtacaagctgatgtgtgaatctgcataaaaaatagcatatgataagctctggcaaagcaactaacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA

-taaaaaa
- - - - - - - - - - gctgatg
- - - - - - - - - - - - - - - - - ctgcata
- - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactaa