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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcctgcatgctcaagcccgaaatacaagtaaggtactggagatttatgaaacagattaatagttccagggtttccaaactgtaaatacataaat...

Basic information

species Zea mays
transcript GRMZM2G069916_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069916_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 10
TGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcctgcatgctcaagcccgaaatacaagtaaggtact-ggagatttatgaaacagattaatagttccagggtttccaaactgtaaatacataaat----
||||||||| ||||||||||||||||| || ||  ||||  | || |||||||||||||||||||||| ||||||||| |||||| |||| ||||| | | |      |   ||||||| ||  | || || | ||  ||   ||| | | |||||    |      |  ||||  |||||      
TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGgtacattcttgcatacccgactt---accgcaagtaaagtttttggggaatgat--aattaatttagaattccaaatgtctactgccctaaaggcataatcacaa
















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|13178061|gb|BG349319.1|BG349319
EST:     CTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: CTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|60349607|gb|DN216580.1|DN216580
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|32847638|gb|CD987319.1|CD987319
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|94476347|gb|EB705305.1|EB705305
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|149000972|gb|EE038212.2|EE038212
EST:     AAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|32847430|gb|CD987111.1|CD987111
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|32832751|gb|CD972429.1|CD972429
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAA
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAA
EST: gi|32835473|gb|CD975151.1|CD975151
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|88756296|gb|DY540437.1|DY540437
EST:     AAACAGAAAGAACTTCAG                         GAGCAGGGAAATAAAAGGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAA-GGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|60340812|gb|DN207785.1|DN207785
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|32834150|gb|CD973828.1|CD973828
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|13178510|gb|BG349768.1|BG349768
EST:     GGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: GGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|60400106|gb|DN232913.1|DN232913
EST:     AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: AATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|13178184|gb|BG349442.1|BG349442
EST:     ACATGCTGATTCG-GAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: ACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
EST: gi|16377976|gb|BI992214.1|BI992214
EST:     CTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG                         GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG
genomic: CTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG

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), 47 (downstream exon)
Score: 64

TGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 54

TGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 50

TGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

TGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcct ... caccttgcagGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGgtaaattcctgcatgctcaagcccgaaatacaagtaaggtactggagatttatgaaacagattaatagttccagggtttccaaactgtaaatacataaat

- - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatacaa