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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgccaatacattccatttgactcatttgatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT

Basic information

species Zea mays
transcript GRMZM2G492252_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G492252_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16570.2 (Oryza sativa), 3'ss of exon 5
---gtgtgcca-atacattccatttgactcatttgatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgttt-cagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT
    |   |   || || |    || | |||| |  || ||   | |   ||||| || | |      || |      ||||| || ||||||||||  | || || ||  ||||||| ||||||||||  |||| |||||| ||||||||||||||||||||| |||||||||| |||||||| || ||
gtgatacactttattcacttaggttaattcatatactgcttcttact--ctcctgcaagcattacattgtagctgatgttttgcttgcagATTATGATGCCCTTAGGGCCTTGGATGCAGACAATAGCCCTCATGCTCCTTCGATGAGTGAAGAAGAAATAAATGCTCTTCCTGTATTCAAATACAAGGT
















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|78074674|gb|DV503108.1|DV503108
EST:     CCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: CCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|60359234|gb|DN226207.1|DN226207
EST:     GACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|78123225|gb|DV541609.1|DV541609
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|149105940|gb|EE291566.2|EE291566
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|88758241|gb|DY542382.1|DY542382
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|71424496|gb|DR806334.1|DR806334
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|110517661|gb|EE022248.1|EE022248
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|88758240|gb|DY542381.1|DY542381
EST:     AGACTTCAACTGGCTCTTTTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCGGACAATAGCCTGCATGTTCCTT
genomic: AGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|50324565|gb|CO519691.1|CO519691
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGAC
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGAC
EST: gi|71774882|gb|DR972760.1|DR972760
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|91868647|gb|EB400100.1|EB400100
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|71426202|gb|DR807252.1|DR807252
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|71774881|gb|DR972759.1|DR972759
EST:     AGCCTTAGACTTCAACT-GCTTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: AGCCTTAGACTTCAACTGGC-TCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|60352872|gb|DN219845.1|DN219845
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|86467860|gb|DY234230.1|DY234230
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
EST: gi|148971543|gb|EE022249.2|EE022249
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGANCA-TAGCCTGCATGTTCCT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGA-CAATAGCCTGCATGTTCCT
EST: gi|76936255|gb|DV174660.1|DV174660
EST:     GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAG                         ATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT
genomic: GAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTT

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), 48 (downstream exon)
Score: 96

CGTGTGCATGTACCGCCGACCATTGCCCTTGCTACGAGAGGCCAGTTACAGAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 11

CGTGTGCATGTACCGCCGACCATTGCCCTTGCTACGAGAGGCCAGTTACAGAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 24

CGTGTGCATGTACCGCCGACCATTGCCCTTGCTACGAGAGGCCAGTTACAGAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 25

CGTGTGCATGTACCGCCGACCATTGCCCTTGCTACGAGAGGCCAGTTACAGAGCCTTAGACTTCAACTGGCTCTTCTTGACCGTGAATTTGATGATTTAGgtgtgccaat ... tttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT
 atttgat  putative branch site (score: 25)
                                        ttctttttgtttc  putative PPT
                                      aattctttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgccaatacattccatttgactcatttgatggtttacagtgtttcctgaaaacttagtgacgtggaattctttttgtttcagATTATGACACTCTGAGAGCACTGGATGCTGACAATAGCCTGCATGTTCCTTCTATGAGTGAAGAAGAAATAAATTCTCTTCCTGTCTTCAAATATAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA