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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcttgctgattagtgtttctttgcataacccttattttggaggttgagtaaatgttcttctttaccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG

Basic information

species Zea mays
transcript GRMZM5G879882_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 6
gtatgtgcttgctgattagtgtttctttgcata---acccttattttggaggttgagtaaa-tgttcttctttaccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG
||| ||| |   | | || | |||||| | |||   | |||||||||| |  ||| ||||| | | | | | |||    ||||||| | ||| || ||||| ||||||||||||||||| |||||||| || || |||
gtaggtgttg--taactatt-tttcttagtataataatccttattttgaattttgggtaaaatatgcctgtgtactttgtctagGTATACATCATTGGAGGGGATGGAACTCAGAAGGGAGCATATGAAATATATAAG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 6
gtatgtgcttgctgattagtgtttctttgcataaccct---tattttggaggttgagtaaatgttcttctttaccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG
|| ||  |||  |  | | |||  |  |  |||    |   |    || | ||  |  | ||     ||| |   |  |  |||| |  || || |||||||||||||||||||||||||||| ||  ||||   ||
gtctgcacttctt--tcaatgtagcagtatatatttttgtgtgccgtgtaagtacatcagattaatatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 6
gtatgtgcttgctgattagtgtttctttgcataacccttattttggaggttgagtaaatgttcttctttaccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG
               |  |  |||||||  ||    |   |  || | ||  |  | ||   | ||| |   |  |  |||| |  || || |||||||||||||||||||||||||||| ||  ||||   ||
--------------gtctgcatttctttctatttagca-gtagtgtatgtacatcagattaacatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG

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|87153557|gb|DY398346.1|DY398346
EST:     ATGATACCAAAAAGATCGTTGACAACATTCAAGATCGTGGAATTAATCAG                         GTGTACATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
genomic: ATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
EST: gi|8367787|gb|BE050732.1|BE050732
EST:     ATGATACCAAAAAGATCGTTGACAACATTCAAGATCGTGGAATTAATCAG                         GTGTACATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
genomic: ATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
EST: gi|19351112|gb|BM895644.1|BM895644
EST:     ATGATACCAAAAAGATCGTTGACAACATTCAAGATCGTGGAATTAATCAG                         GTGTACATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTCC
genomic: ATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
EST: gi|33942634|gb|CF349234.1|CF349234
EST:     GTTGACAACATTCAAGATCGTGGAATTAATCAG                         GTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
genomic: GTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
EST: gi|19436208|gb|BM952618.1|BM952618
EST:     ATGATACCAAAAAGATCGTTGACAACATTCAAGATCGTGGAATTAATCAG                         GTGTACATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC
genomic: ATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTAC

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: 47 (upstream exon), 47 (downstream exon)
Score: 199

TGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCACGAGGTGGCCATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

TGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCACGAGGTGGCCATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 200

TGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCACGAGGTGGCCATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 132

TGATATCCACAAACGAGGTGGTACAGTTCTTGGAACATCACGAGGTGGCCATGATACCAAAAAGATTGTTGACAACATTCAAGATCGTGGAATTAATCAGgtatgtgctt ... ccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcataacccttattttggaggttgagtaaatgttcttctttaccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG
   gcataac  putative branch site (score: 132)
                                 tgttcttctttacc  putative PPT
            ttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcttgctgattagtgtttctttgcataacccttattttggaggttgagtaaatgttcttctttaccacatctagGTGTTCATTATAGGAGGAGATGGAACTCAGAAGGGTGCATATGAGATTTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA