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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcttgcttgaaattggaaagagcgtagattgatactgttggtcgattgctatttttaaagcatattagcctatatgcttggtgatgcaccatttacaacatttatttaacctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA

Basic information

species Zea mays
transcript GRMZM2G558539_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G558539_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08980.4 (Oryza sativa), 3'ss of exon 3
gtttgtcttgcttgaaattggaaagagcgtagattgatactgttggtcgattgctatttttaaagcatattagcctatatgcttggtgatgcaccat-ttacaacatttatttaacctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA
                             |   |||   ||  |  ||      |   || |      | |  ||| | || |  |  || ||  || |||      ||  |   | | ||| |||| || |||||  ||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| 
-------------------------tatttctgttgtagcttatt-tcagaaattggcttaattaaccagtgacctctttgatcagacattcatgatgttagtgttcttgatcttcttttttgcagGGGTGTCAGGTTTGATAGTACCTGCAGCAACTGTTGGAGCACTCGGTTATGGTTACATGTGGTGGAAG
















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|211477919|gb|FL000313.1|FL000313
EST:     TGCTAATTCACGACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATG
genomic: TGCTAATTCACAACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAGgtttgtcttg ... ctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATG
EST: gi|211480805|gb|FL000335.1|FL000335
EST:     TGCTAATTCACAACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAG                         GAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATG
genomic: TGCTAATTCACAACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAGgtttgtcttg ... ctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATG

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), 49 (downstream exon)
Score: 219

GTGCGCCGCCTTGCCATGGAGATCCGGCAACTTGCTAATTCACAACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAGgtttgtcttg ... ctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

GTGCGCCGCCTTGCCATGGAGATCCGGCAACTTGCTAATTCACAACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAGgtttgtcttg ... ctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 397

GTGCGCCGCCTTGCCATGGAGATCCGGCAACTTGCTAATTCACAACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAGgtttgtcttg ... ctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

GTGCGCCGCCTTGCCATGGAGATCCGGCAACTTGCTAATTCACAACCAATAACTGTTCTCAATGGAGGTTCTGGACAATCAGgtttgtcttg ... ctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcctatatgcttggtgatgcaccatttacaacatttatttaacctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA
                                      atttaac  putative branch site (score: 314)
                                       tttaacctcttttc  CT-rich tract
                         atttacaacatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcttgcttgaaattggaaagagcgtagattgatactgttggtcgattgctatttttaaagcatattagcctatatgcttggtgatgcaccatttacaacatttatttaacctcttttcagGAGTATCAGGCCTGATAGTACCTGCAGCAACTGTTGGAGCACTAGGTTATGGTTATATGTGGTGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA