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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGAACTTGGTTTCACTTTTTCCTTCCCGGTGAACCAAACATCAATATCATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaattgaaacaattttacctaattcgatctattgaataccttcctatagttcagtaaggccttatttggttattcgtatcccatgtggataggat...

Basic information

species Zea mays
transcript GRMZM2G058745_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058745_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g44760.1 (Oryza sativa), 5'ss of exon 3
GAGAGAACTTGGTTTCACTTTTTCCTTCCCGGTGAACCAAACATCAATATCATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaattgaaacaattttacctaattcgatctattgaataccttcct-atagttcagtaaggccttatttggttat-tcgtatcccatgtggataggat-
|||||| || || ||||| ||||||||||| |||| ||| ||||||||||| |||||||| |||||||||||||||||||| || |||||||||| | ||||||||     ||| || |||     || |  |   | ||| ||  |||| ||  |||  |||   | |      |||| ||  |       | ||||     
GAGAGAGCTGGGCTTCACCTTTTCCTTCCCAGTGAGCCAGACATCAATATCGTCAGGAACGCTCATCAAGTGGACAAAGGGTTTCTCCATCAATGACGCGgtaaaagtcaaaaataacttttggacataccctgactagaacacaatcctgatccttctttaaacacatg---aattatgtcacaaggttccttgataaagct
















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|18661550|gb|BM501458.1|BM501458
EST:     CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACG                         GTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGG
genomic: CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
EST: gi|148951791|gb|EC897551.2|EC897551
EST:     CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACG                         GTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
genomic: CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
EST: gi|149104506|gb|EE289955.2|EE289955
EST:     CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACG                         GTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
genomic: CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
EST: gi|148968085|gb|EE019415.2|EE019415
EST:     CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACG                         GTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
genomic: CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
EST: gi|71772829|gb|DR970754.1|DR970754
EST:     CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACG                         GTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA
genomic: CATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGA

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: 182

GAGAGAACTTGGTTTCACTTTTTCCTTCCCGGTGAACCAAACATCAATATCATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGACTAGATATGAAAGCTACGGCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 455

GAGAGAACTTGGTTTCACTTTTTCCTTCCCGGTGAACCAAACATCAATATCATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGACTAGATATGAAAGCTACGGCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 514

GAGAGAACTTGGTTTCACTTTTTCCTTCCCGGTGAACCAAACATCAATATCATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGACTAGATATGAAAGCTACGGCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1128

GAGAGAACTTGGTTTCACTTTTTCCTTCCCGGTGAACCAAACATCAATATCATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaatt ... cctgaatcagGTTGGTGAAGATGTTGTTTCTGAGTTGAGCAGGGCCATGGAGAGGCAGGGACTAGATATGAAAGCTACGGCATTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGAACTTGGTTTCACTTTTTCCTTCCCGGTGAACCAAACATCAATATCATCAGGAACACTCATCAAGTGGACAAAGGGCTTTTCCATCAATGGCACGgtaaaaaattgaaacaattttacctaattcgatctattgaataccttcctatagttcagtaaggccttatttggttattcgtatcccatgtggataggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA