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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtgattcctcccacaataggttctgctattaggttgtgcacgtcagtcatgtttcgtgtattattttaatcgctgaatgggtcatactggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG

Basic information

species Zea mays
transcript GRMZM2G064695_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g40830.3 (Oryza sativa), 3'ss of exon 1
gggtgattcctcccacaataggttctgctattaggttgtgcacgtcagtcatgtttcgtgtat-tattttaatcgctgaatgg--gtcatactggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG
     |||| |  |    ||| |  | | |||| |||||  ||   |    |  || |||||| || |   |    | | ||    |  ||      ||||||  |||||| | |||||||||||| |||| ||||||||||||||| |||| |||||||||||||||
--tcaattcttttcttcgtag-tcattcaattaagttgtatactatacatgttatttgtgtatgtactcctacttttaagtgtttatgttatctcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG
















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|211374289|gb|FL290759.1|FL290759
EST:     GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAA                         GTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
genomic: GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
EST: gi|71760334|gb|DR958271.1|DR958271
EST:     GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAA                         GTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
genomic: GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
EST: gi|149076126|gb|EE164711.2|EE164711
EST:     GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAA                         GTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
genomic: GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
EST: gi|148935326|gb|EC879367.2|EC879367
EST:     GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAA                         GTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
genomic: GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
EST: gi|148951069|gb|EC896728.2|EC896728
EST:     GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAA                         GTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA
genomic: GCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAA

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), 49 (downstream exon)
Score: 733

AGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 685

AGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 497

AGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 814

AGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgt ... ggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtcatgtttcgtgtattattttaatcgctgaatgggtcatactggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG
                    ttttaat  putative branch site (score: 814)
             tgtattattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtgattcctcccacaataggttctgctattaggttgtgcacgtcagtcatgtttcgtgtattattttaatcgctgaatgggtcatactggtactgcagGTAAAATGTTAGGCCAGATTCTGATAACGAAACAAACTGGTCCAGAGGGAAAGATTGTGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - -cccacaa
- - - - - - - - - - -gttctgc
- - - - - - - - - - - - - - - - - - -gtgcacg
- - - - - - - - - - - - - - - - - - - - - - - - - atgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatg