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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG

Basic information

species Zea mays
transcript GRMZM2G551402_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 7
agaaaaaaatgcttgtctttttatgtgaaagtattctat---actgcatgatct-gcatatccttgtatactgtctctgaattttc----acctcatgttg-cgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG
        ||| || |   ||| |||  || ||| || |   | |  |    || ||| |   ||    | |   | |  |||||     |  | ||  || |   ||||||||||||||||||||| |||||||| ||||||||| |||||||||| |||||||| ||||| |||||||| ||||||
--------atgattatgccttt-tgtcgaactatgctgttgaattttacatcctagcaaacagttcccaattcattatagatttttgaaaatgttatcctgtctaccagGTATAAATTTGATGATGAGCGTGTAACTAAAGAAGATACTAAGAAGGCCCTTGAAGAGCAATACGGGGGTGAGGAAGAG

upper sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 7
---agaaaaaaatgcttgtctttttatgtgaaagtattctatact-gcatgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG
    |  |   ||  |    ||| || | ||||| ||    | || | ||| |   |  |   |   | | |||||   |  | | |    |   |    |||||| ||||||||| ||||| || ||||||||||||||  | |||| |||| | |||||||| ||||| ||||| ||||||
tcttgtcactgat-ttaaaatttgtaag-gaaagcataacttgcttgtatgttgatccaactttcccaaaatgtct--aagctgttaggcaacacttgtttcagGTTTAAATTTGACGATGAGCGAGTAACAAAAGAAGAATCCAAGAGGGCTTTGGAAGAACAGTATGGTGGTGAAGAAGAG

upper sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 11
agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatc----cttgtatactgtctctgaattttcacctcatgttgcgc----tcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG
        | |||  | || ||     |    |  |  |  ||||   | | || |||     ||||  | | | ||| | |       |||   | | |    ||||||||||||||||||||||||| ||||| || ||||||   || | |||| | || || |||||||| ||||| ||||||
-------tacgctgatgttatt-cacaaggtcacacgtttttgcaatttgtccaaatcatgttttgtgcattttttctcattaactcgttcaaacttctccttttcagGTATAAATTTGATGATGAACGAGTAACCAAGGAAGATTTGAAAAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG

upper sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G11910.1 (Arabidopsis thaliana), 3'ss of exon 11
agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatccttgtatactgtctctgaattttc--acctcatgttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG
   ||| ||   ||   |  || ||||    ||      ||||    |      | |    ||    |   | | || | ||  | ||  |  | |  |||||||||||||||| |||||||| || || ||||||||||  || |  || || ||||| |||||||| ||||| ||||||
-ataaataactattacgtccttttgtggttttagatggcactgttgaaaacattt-tgtcagtgccttacttttaaactatctaaacttctaattctttcagGTATAAATTTGACGATGAACGGGTCACGAAAGAAGATGTCAAAAGAGCACTGGAAGAGCAATATGGTGGTGAAGAAGAG

upper sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgc---tcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG
       | |   | |  |||||  | |  || |   ||  |      |       |   |||||  | | |   || |||||  |   |||       | ||||  ||||||||||||||||| || ||||||||||||  ||||| ||| || || || || ||||| ||||| ||||||
--ttttgattttctattatttta-attatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG

upper sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 11
-----agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG
     |   |  | | | ||   |   || || |  ||  ||| | |   |   || ||  |      || |||| |   ||   | || |     |    ||||||||||||||||||||||| | || ||||||||||| |  |||| |||| | || || |||||||| ||||| ||||||
aatgtatggatgagtacatgcaatgccatttgtagctaagctacaattt-taccctacagttgtc---atgctgtataaaaagaataacttgggaattt-ttcagGTATAAATTTGATGATGAAAGGGTGACAAAAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG

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|166595819|gb|EG038985.1|EG038985
EST:     CTTTATCTGAGCAATG                         GTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCT
genomic: CTTTATCTGAGCAATGgtaggcattt ... ttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCT
EST: gi|32937019|gb|CF041838.1|CF041838
EST:     CATGGTGGTCACTACTATGCATTCATACGGCCAACTTTATCTGAGCAATG                         GTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCT
genomic: CATGGTGGTCACTACTATGCATTCATACGGCCAACTTTATCTGAGCAATGgtaggcattt ... ttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCT

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), 49 (downstream exon)
Score: 169

TGTTCTTGTTCATAGTGGTGGGGTACATGGTGGTCACTACTATGCATTCATACGGCCAACTTTATCTGAGCAATGgtaggcattt ... ttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

TGTTCTTGTTCATAGTGGTGGGGTACATGGTGGTCACTACTATGCATTCATACGGCCAACTTTATCTGAGCAATGgtaggcattt ... ttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

TGTTCTTGTTCATAGTGGTGGGGTACATGGTGGTCACTACTATGCATTCATACGGCCAACTTTATCTGAGCAATGgtaggcattt ... ttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 67

TGTTCTTGTTCATAGTGGTGGGGTACATGGTGGTCACTACTATGCATTCATACGGCCAACTTTATCTGAGCAATGgtaggcattt ... ttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG
                            tgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgctcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- aaaaaaa
- - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - -ctgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtat