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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattattatagttattttccagatactgaggaacccaagctgcatgaaaggttgaatttaatatatttccatcttgctctactgatttccaccattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA

Basic information

species Zea mays
transcript GRMZM2G016827_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016827_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g20270.1 (Oryza sativa), 3'ss of exon 5
----tatta--ttatagttattttccagatactgag-gaacccaagctgcatgaaaggttgaatttaatatatttccatcttgctctactgatttccaccattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA
    | ||    |  | |||| ||    || ||| | |     |   ||| |      |||||| |  ||| | ||   ||| |  ||||| |||       | |||| |||||||||||||  ||||| ||||| ||||| ||||||||||||| |||||||||||||||||||||||||||||||||||| ||||| ||| ||||
agtttgttgagcttgaattatattttgcatcctgtgtgttgatagattgcctttctatttgaatattctatgtatcttacttacaatactgtttt-------tgcagTAATTGAGGAACTCAACGCTACAGGAAAATTTGATTTTATGGACCTTAGTGTGGATGAAGCTGAACATAGCATGGAAATGCATTTACCCTATCTTTCTAA

upper sequence: GRMZM2G016827_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G13970.1 (Glycine max), 3'ss of exon 4
tattattatagtt-attttccagatactgaggaacccaagctgcatgaaaggttgaatttaatatatttccatcttgctctactgatttccaccattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA
|  ||   || || |||| |     |||||   |      ||     |  | ||   | |    |  || | ||    |   |   ||   |   | ||||| | |||||| || |  ||||| || || |||||  | |||||  ||  ||| |||||||||||||||||||||||||||||  |||| || ||||| ||
tggtagattatttgatttactgagaactgattcattttgactttgatattgattctttctttcctcattgc-tcacatttggcactttgttattttaccagTAACTGAGGAGCTTAAAGCTACGGGGAAATTTGAGCTGATGGATATTCGTGTTGATGAAGCTGAACATAGCATGGAAATGCACCTGCCATATCTTGCCAA

upper sequence: GRMZM2G016827_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g06320.t01 (Vitis vinifera), 3'ss of exon 6
tattattatagttattttccagatactgaggaacccaa-gctgcatgaaaggttgaatttaatatatttccatcttgctctactgatttccaccattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA
|   |   ||  |||||  |    |   ||          |  |||     | ||  ||  | | | ||  ||     ||   |   ||     ||  ||||| ||||||| || |  ||||| ||||| |||||| | ||||| ||| | || ||||||||||||||||||||||||||||||||||| || ||||||||
ttcgacactatgtatttgtctagaatgaagatgtttgtcaccacatatcttgctgt-ttggagaaagtttgataacattcatgtttgtttttttatgtcagTCGTTGAGGAGCTAAAAGCTACAGGAAAATTTGAACTGATGGATCTTGACGTTGATGAAGCTGAACATAGCATGGAAATGCATTTGCCATATCTTGCTAA

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|211322017|gb|FL082184.1|FL082184
EST:     GGCTTCTGTTTACTGTACCCCAATTGGGGATTTGCCAGTAGACCAGGAAG                         TCATCGAGGAACTCAGTGC
genomic: GGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAGgtgagtgttt ... accattccagTCATTGAGGAACTCAGTGC
EST: gi|78107484|gb|DV525902.1|DV525902
EST:     GGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAG                         TCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATG
genomic: GGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAGgtgagtgttt ... accattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATG
EST: gi|211152189|gb|FL082181.1|FL082181
EST:     GGCTTCTGTTTACTGTACCCCAATTGGGGATTTGCCAGTAGACCAGGAAG                         TCATCGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATG
genomic: GGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAGgtgagtgttt ... accattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATG

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: 257

CTGCTTGGCCCTTCTCATCACTACTACACTCCAAAATGTGCTTTAACCAGGGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAGgtgagtgttt ... accattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

CTGCTTGGCCCTTCTCATCACTACTACACTCCAAAATGTGCTTTAACCAGGGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAGgtgagtgttt ... accattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 439

CTGCTTGGCCCTTCTCATCACTACTACACTCCAAAATGTGCTTTAACCAGGGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAGgtgagtgttt ... accattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 466

CTGCTTGGCCCTTCTCATCACTACTACACTCCAAAATGTGCTTTAACCAGGGCTTCTGTCTACTGTACCCCAATCGGGGATTTGCCAGTAGACCAGGAAGgtgagtgttt ... accattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaggttgaatttaatatatttccatcttgctctactgatttccaccattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA
                                  tactgat  putative branch site (score: 466)
                                        tttccacc  CT-rich tract
      ttgaatttaatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattattatagttattttccagatactgaggaacccaagctgcatgaaaggttgaatttaatatatttccatcttgctctactgatttccaccattccagTCATTGAGGAACTCAGTGCTACTGGAAAGTTTGAATTTATGGACCTTAATGTGGATGAAGCTGAACATAGCATGGAAATGCATTTGCCCTACCTTGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - -gatactg
- - - - - - - - - - - - - - - -aacccaa
- - - - - - - - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatt