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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtatgcatactaccgaccttattgctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG

Basic information

species Zea mays
transcript GRMZM2G051842_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051842_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 5
gtctgtatgcatactaccgaccttattgctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG
|||||   |||    |  |    ||  |   | ||    ||   |    |   ||  | |  || || ||   ||  |  |||||||| ||||||| |||| |  | || ||| |||||||||| || || ||||||||||||||||| |||||||||||||||||||||||| || ||||
gtctgaccgcagctcattgg---taccgtaaggtctttttttggtacaggcacca-gtctgattttgtttatttattacacagATGGTTCGTGACTATAGGACACAACTCATTGACCTTTTGGAAACTGGCAACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG

upper sequence: GRMZM2G051842_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 5
---------------gtctgtatgcatactaccgaccttattgctcgct-cgaagttaactttctgtctcatatttctttgtgattgcctaccatg--cagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG
                |    |||||    | |   ||| ||      | |   || |   || | |||  ||   | |||   ||   |||| ||  |||||||| ||  ||| |||       ||| |  |  |  || |  | ||  | || || |||||||| ||||||||||||||||| |||||| |  || |
tttgactgcagtatcctactcatgcactggaacagacttgttctgaattgctgggtaaggattgtctcttttaac-cattgcttttttttaccttggccagATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG
















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|71446345|gb|DR827395.1|DR827395
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTG
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTG
EST: gi|60338856|gb|DN205829.1|DN205829
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|91057161|gb|EB167579.1|EB167579
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGG
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGG
EST: gi|29543849|gb|CB604229.1|CB604229
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|31612067|gb|CD568689.1|CD568689
EST:     TTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|76293563|gb|DV033131.1|DV033131
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|76286678|gb|DV026246.1|DV026246
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTAATAACCTTTTTGGAGACCGGTAA
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTT-GGAGACCGGTAA
EST: gi|71771409|gb|DR969346.1|DR969346
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGA
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGA
EST: gi|71762333|gb|DR960270.1|DR960270
EST:     CTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: CTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|78105422|gb|DV523840.1|DV523840
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTTTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|211123067|gb|FL031406.1|FL031406
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|29543893|gb|CB604273.1|CB604273
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|148987163|gb|EE030992.2|EE030992
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGAC
EST: gi|71447665|gb|DR828715.1|DR828715
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGGTA-
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGG-TAA
EST: gi|78103938|gb|DV522356.1|DV522356
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|101385265|gb|EB814678.1|EB814678
EST:     TAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|149088934|gb|EE178077.2|EE178077
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
EST: gi|148959742|gb|EC905640.2|EC905640
EST:     TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAG                         ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC
genomic: TTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAAC

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: 39 (upstream exon), 49 (downstream exon)
Score: 288

TGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

TGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 122

TGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 132

TGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCAGTTTTGAGgtctgtatgc ... taccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG
         agttaac  putative branch site (score: 132)
                          atatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtatgcatactaccgaccttattgctcgctcgaagttaactttctgtctcatatttctttgtgattgcctaccatgcagATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG