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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

Basic information

species Zea mays
transcript GRMZM2G134770_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134770_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
-----------atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
           |  ||  ||   | ||||| |  ||||||  | ||||||        ||| |  ||   | ||||||||  ||  ||     | ||| || |  ||  |||||||||||  ||||| || ||||||||||| ||| |||||||||||||||||||||| ||||| || ||||| || |||||    || |  || |||||
ccacattgcataagttatgcgtgtcactta-gcactagttcttgtaatggc-------tttgtccttt--ttaattctatataatctttacatctaatatt-tcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA

upper sequence: GRMZM2G134770_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 8
atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
                   || | |  ||| |    || |   || |||   | || ||| || | |    |   | |||     |  | ||||    ||||| |||||  || || || ||||||||||||||| |||| |  |||||||||||||| ||| |||| || |||||| | |   | ||||| || || ||
------------------gtgagttcttttttaacttgctgctattattggct-ttgcattaactttg---atgctaacat----aattcatttattcagAACAAAAGATGCCTGATGGAAGTTGGAAGTGTGAGAAGTGTAGCAACATAAACTATCCCTTCAGAACCAAGTGCAATAGACAGAACTGTGGGGCCGATAA
















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|5005812|gb|AI711874.1|AI711874
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|71428348|gb|DR809398.1|DR809398
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|89248611|gb|DY620397.1|DY620397
EST:     GAAAACCAGGGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GAAAACCAGGGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|12970927|gb|BG267228.1|BG267228
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32943442|gb|CF048261.1|CF048261
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|28910525|gb|CB331482.1|CB331482
EST:     AAACCAGGGATCTAAGCCTGATGG-TTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAG-GTGAGCAG-GCAATAACATAA
genomic: AAACCAGGGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|94474683|gb|EB703641.1|EB703641
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|78112738|gb|DV531132.1|DV531132
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32841271|gb|CD980952.1|CD980952
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32839908|gb|CD979589.1|CD979589
EST:     GGATCTAAGTCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGC
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGC
EST: gi|74243768|gb|DT651682.1|DT651682
EST:     ACCAGGGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACCCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: ACCAGGGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|88752563|gb|DY536704.1|DY536704
EST:     GGATTTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTGGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|211158909|gb|FK993540.1|FK993540
EST:     GGWTCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCWATKACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32841323|gb|CD981004.1|CD981004
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32835369|gb|CD975047.1|CD975047
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32840727|gb|CD980408.1|CD980408
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|78026571|gb|DV494958.1|DV494958
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|31350190|gb|CD434547.1|CD434547
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGGGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32841497|gb|CD981178.1|CD981178
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|89247194|gb|DY618980.1|DY618980
EST:     GGATCTAAGCCTGATGGTTTAAGAGGGTCAA                         AACCAAAGACACCAGAGGGCAGTGGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 247

GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 113

GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA


Block sizes: 36 (upstream exon), 47 (downstream exon)
Score: 178

GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA


Block sizes: 31 (upstream exon), 47 (downstream exon)
Score: 107

GGATCTAAGCCTGATGGTTTAAGAGGGTCAAgtaagtttcc ... attttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
                                         tcttatttt  CT-rich tract
                aattctattcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - -gcacata