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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttgatgcttgcttcagcactcgttgctatatattatatatttttgcgttgttataagatctaaggatgttgaccgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA

Basic information

species Zea mays
transcript GRMZM2G051043_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051043_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 2
gtgagtacttgatgcttgcttcagcactcgttgctatatattatatatttttgcgttgttataagatctaaggatgttgaccgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
||||||| |||| | ||  |  |            ||  || |  |||| | | |  | | | |  ||| | || | ||| | ||||||||||||| |||||||||||||||||||| ||| | | ||||||||||
gtgagtagttgaggatttttctaag---------catgcat-acgtattctagaggagctgttatgtctgatga-gctgagcatctgttagGTGACGGAGGAGAGACTTGCTGATATATTTGCTAACTGTGGGCAA
















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|108823990|gb|EC277998.1|EC277998
EST:     GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACT                         GTGACAGAGGAGAGGCTTGCTGATATCTTTACCACCTGTGGGCAA
genomic: GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
EST: gi|108953255|gb|EC364659.1|EC364659
EST:     GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACT                         GTGACAGAGGAGAGGCTTGCTGATATCTTTACCACCTGTGGGCAA
genomic: GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
EST: gi|4730461|gb|AI649627.1|AI649627
EST:     GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACT                         GTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
genomic: GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
EST: gi|38502629|gb|CF972489.1|CF972489
EST:     GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACT                         GTGACAGAGGAGAGGCTTGCTGATATCTTTACCACCTGTGGGCAA
genomic: GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
EST: gi|4730460|gb|AI649626.1|AI649626
EST:     GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACT                         GTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
genomic: GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
EST: gi|33771172|gb|CF272833.1|CF272833
EST:     GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACT                         GTGACAGAGGAGAGGCTTGCTGATATCTTTACCACCTGTGGGCAA
genomic: GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
EST: gi|78077711|gb|DV506143.1|DV506143
EST:     GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACT                         GTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
genomic: GAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA

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), 45 (downstream exon)
Score: 139

CATCAACCAAGGAAGGAGGAGGACAAATGGTAGAGTGAGGCGGGCAGACAGAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 99

CATCAACCAAGGAAGGAGGAGGACAAATGGTAGAGTGAGGCGGGCAGACAGAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 152

CATCAACCAAGGAAGGAGGAGGACAAATGGTAGAGTGAGGCGGGCAGACAGAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 285

CATCAACCAAGGAAGGAGGAGGACAAATGGTAGAGTGAGGCGGGCAGACAGAGAGGACAGCATTAGGCGAACTGTTTATGTCTCTGAACTTGACCATACTgtgagtactt ... cgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattatatatttttgcgttgttataagatctaaggatgttgaccgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA
                                      tgttgac  putative branch site (score: 285)
     tatatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttgatgcttgcttcagcactcgttgctatatattatatatttttgcgttgttataagatctaaggatgttgaccgtctgttagGTGACAGAGGAGAGACTTGCTGATATCTTTACCACCTGTGGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT