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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtctagctttaatttccgccatgtctcagttcttccatgcagactaatatattatatactaagcatatatatacatactaatgcag

Basic information

species Zea mays
transcript GRMZM2G059083_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059083_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g01340.2 (Oryza sativa), 5'ss of exon 2
GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagtt----gtctagc--tttaatttccgccatgtctcagttcttccatgcagactaatatattatatactaagcatatatatacatactaatgcag
|| ||||||||||||||||||||||| ||||||||||||||||| ||| ||||||||||||||||||| |||||||||||| || |    ||||     | ||||  | |  |  |    || |||   |||  | ||||  | ||||   ||                         
GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCTgtaagctaggagtctgatcatgtaatagcagttagatt---gtacttgtgtgctaattaatggagtataatttag------------------------
















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|78085944|gb|DV514337.1|DV514337
EST:     CCCCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|13150081|gb|BG320403.1|BG320403
EST:     ACCAACGATCAGGGGGAGGTCGTCAAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: ACCAACGATCAGGGGGAGGTCGTC-AAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|78021596|gb|DV489983.1|DV489983
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|78085945|gb|DV514338.1|DV514338
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|89253046|gb|DY624832.1|DY624832
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAAATTCCTCT                         GTGACTTGAAGCCAGGCGCTGAAGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|13315987|gb|BG410434.1|BG410434
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGTATTATCACAGGGCCAGTGGGCAAG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTG-AAGATCACAGGGCCAGTGGGCAAG
EST: gi|13315986|gb|BG410433.1|BG410433
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGTTTTTTGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|76015965|gb|DT943135.1|DT943135
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|71420120|gb|DR805018.1|DR805018
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|6918750|gb|AW400280.1|AW400280
EST:     CGAACTTCCTCT                         GTGACTTGAA-CC-GGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|13382263|gb|BG458938.1|BG458938
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|13126400|gb|BG316970.1|BG316970
EST:     CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
genomic: CACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG
EST: gi|76015964|gb|DT943134.1|DT943134
EST:     TCAGGGGGAAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT                         GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGGGGGCAAGG
genomic: TCAGGGGG-AGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGG

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 7 RNA-Seq libraries.


Block sizes: 36 (upstream exon), 46 (downstream exon)
Score: 15

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 2

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 187

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG


Block sizes: 18 (upstream exon), 32 (downstream exon)
Score: 1

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG


Block sizes: 30 (upstream exon), 31 (downstream exon)
Score: 3

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 102

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG


Block sizes: 33 (upstream exon), 32 (downstream exon)
Score: 7

GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtc ... actaatgcagGTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCTgtcagttgtctagctttaatttccgccatgtctcagttcttccatgcagactaatatattatatactaagcatatatatacatactaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG