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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacacacaacccaccctgatttgggttagggtttccaacattatgtacacttgtaagattttatatatgaaatgctttgattgaggctgttctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG

Basic information

species Zea mays
transcript GRMZM2G069676_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g26610.2 (Oryza sativa), 3'ss of exon 2
aacacacaacccaccctgatttgggttagggtttccaa---cattatg-tacacttgtaagattttatatatgaaat-gctttgattgaggctgttctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG
            |     ||||  ||||  | |    |     || || | ||    | |  | ||||  || || | |||||  |     || ||  |   |||||||||||||||||||||||||| |||||| ||||| ||||| || || ||||| ||   ||| ||| |||| |||||| | || |||||||||||| | 
----tggggtttataacaattttagttaaagctaaagagtttcttgtgctgcatccatgatgtgttattaatcaatttgctttactctcttctatttctca-cagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCTCACTGAGCCTGTTACTGAAGCAATAGCTTCTGCATTTGCTGCATGGTTA

upper sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 3
aacacacaacccaccctgatttgggttagggtttccaacattatgtacacttgtaagattttatatatgaaatgctttgattgaggctgttctttg-----gcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG
   | |||   || | | ||||  | ||  | ||      || | | || ||  | ||   |||  |    || | || ||   |  || | |        ||||||||||||| ||||| ||||||||||| ||||| || || ||||| |  || || |||   || ||  |||| ||||| || || |||| ||| ||| ||
-taatacacttcaacataatttttgctattgcttttt---tttttttcattta-atgagcatatcaagattattcatttatctggaatgatttccatccatgcagTGATATTCGAGGTGTAGCTGTTGCTGGTGTTGAGGGAGAACCTGTTACTCTTACTGAACCAGTTACAGAAGCAATAGCAGCTGCCTTTGGTGCCTGGTTG
















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|32851046|gb|CD990727.1|CD990727
EST:     GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
genomic: GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
EST: gi|71332327|gb|DR803103.1|DR803103
EST:     GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
genomic: GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
EST: gi|76289294|gb|DV028862.1|DV028862
EST:     GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
genomic: GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
EST: gi|18659547|gb|BM500395.1|BM500395
EST:     GTTTCTGAAGCTTCAAAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
genomic: GTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
EST: gi|101389188|gb|EB816549.1|EB816549
EST:     GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT
genomic: GTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCT

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: 46 (upstream exon), 47 (downstream exon)
Score: 62

CTGCTCAAGGTGGCACTGTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

CTGCTCAAGGTGGCACTGTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

CTGCTCAAGGTGGCACTGTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

CTGCTCAAGGTGGCACTGTTGTGTGTTCATCTGAGAAAGTTGAGTTTCTGAAGCTTCAAAATGGCAGgtatgtagtt ... tctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacacttgtaagattttatatatgaaatgctttgattgaggctgttctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG
                             ctttgat  putative branch site (score: 133)
                                         ctgttcttt  putative PPT
     ttgtaagattttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacacacaacccaccctgatttgggttagggtttccaacattatgtacacttgtaagattttatatatgaaatgctttgattgaggctgttctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - cacaacc
- - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaggctg