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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttttgtaccaatttatcttccacacacaatcatgaaaataactagcctgtggcattatatttgtttcattgaactgatggatccttatgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG

Basic information

species Zea mays
transcript GRMZM2G348578_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348578_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g55380.1 (Oryza sativa), 3'ss of exon 3
aatttttgtaccaatttatcttccacacacaatcatgaaaataactagcc--tgtggcattatatt-tgtttcattgaactgatgg---atccttat-gccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG
    ||||     ||  | ||   || |    |     |||| ||||| |  | |||  |||| |  | || ||||| ||| ||||   ||   ||| ||||||||| || || ||||| || ||| || ||||||| ||||| | ||||||||| ||| | || ||||||||||||| ||| |||||| | || ||| ||||||||
---ctttgccatgatccaactggaaccc----tttcagaaatgactagtcattatggtcttatctaatcttgcattgcactaatggtaaattgctattgccaaacagCTCAGGCACATTTCTAAGTTCTGATGAAGATCCAACCGGAACCCTTGCTGAAGTTGAAAAGAAGATTGCAAAGGCCACCATGATCCCTAGACATCATGGG
















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|21760278|gb|BQ635819.1|BQ635819
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|211499061|gb|FL037730.1|FL037730
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|4776430|gb|AI665433.1|AI665433
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|148950085|gb|EC895620.2|EC895620
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|78027558|gb|DV495945.1|DV495945
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|78110902|gb|DV529300.1|DV529300
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|78080612|gb|DV509024.1|DV509024
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|211076164|gb|FL369889.1|FL369889
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTC
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTC
EST: gi|26457639|gb|CA829222.1|CA829222
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|148941852|gb|EC886830.2|EC886830
EST:     CCCTGAGGAAAGGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCCGA
genomic: CCCTGAGGAAAGG-AGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|149009320|gb|EE041386.2|EE041386
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGA
EST: gi|211533533|gb|FL409962.1|FL409962
EST:     GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAG                         TTCGGGAACATTCCTTAGTGCT
genomic: GCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCT

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: 44 (upstream exon), 43 (downstream exon)
Score: 34

GTGAAAATATAGTAAAAACGGCAAAGGAGAGACTTAAGCCATCAACATTAGCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

GTGAAAATATAGTAAAAACGGCAAAGGAGAGACTTAAGCCATCAACATTAGCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GTGAAAATATAGTAAAAACGGCAAAGGAGAGACTTAAGCCATCAACATTAGCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 641

GTGAAAATATAGTAAAAACGGCAAAGGAGAGACTTAAGCCATCAACATTAGCCCTGAGGAAAGGAGAAACCGCAGAGAGTACAAAAGGAATCAGGACAAGgtaaccttaa ... tgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcctgtggcattatatttgtttcattgaactgatggatccttatgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG
                             aactgat  putative branch site (score: 641)
                                       tccttat  putative PPT
           attatatttgtttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttttgtaccaatttatcttccacacacaatcatgaaaataactagcctgtggcattatatttgtttcattgaactgatggatccttatgccaaacagTTCGGGAACATTCCTTAGTGCTAATGAAGACCCAACTGAAACCCTTGCGGAAATCGAGAAGAAGATTGCAAGGGCTACCATGTTACCCAGAAATCATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - tgtacca
- - - - - - - - - - - ccacaca
- - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - -ctgtggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgg