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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACAGGCGCCATGACCGTGATCGGGATAGGGATTATGACCGCTCCCGTGGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctgaataatactcctcgtgtcacaaattataagacatctcccaaattataaggcgtcttagcttttctagatgtatttttttattatgtataca...

Basic information

species Zea mays
transcript GRMZM2G069916_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g62640.5 (Oryza sativa), 5'ss of exon 11
---GGGACAGGCGCCATGACCGTGATCGGGATAGGGATTATGACCGCTCCCGTGGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAG--------CA--Ggtattgctgaataatactc---------ctcgtgtcacaaattata------agacatctcccaaattataa-ggcgtcttagcttttctagat-gtatttttttattatgtataca-------------------------------------------
   ||||| | |||||||| || ||||||||||| ||||||||||| || ||||| |||||||||||||| || || ||||| || ||||||||||||||        ||  ||| |   ||   | | |||         || || |  | | ||||       | | |  |   | | ||||| | |     | |      | ||  | |  ||||  |||| | ||                                            
ATAGGGACCGCCGCCATGATCGCGATCGGGATAGAGATTATGACCGTTCGCGTGGCCATGATTCAAGGAGAAGGGAACGTTCTCGATCCAGGGAGCGCAGgtatggttcaatggtttctttgctcacttctctctgcctttcttgtatagcgatttattccgaccataaacttttgacagtataatgacaaagaaacacaatgaaattatctgcttttgatatggaaacctttatatcactaggagctaacattagacagttgttattttcag
















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|60349607|gb|DN216580.1|DN216580
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|32847638|gb|CD987319.1|CD987319
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGT
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGT
EST: gi|88757903|gb|DY542044.1|DY542044
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|30052552|gb|AI065841.2|AI065841
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|83278840|gb|DV942848.1|DV942848
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|94476347|gb|EB705305.1|EB705305
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCCCGAGAGATACTAAATGTTACCCCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|32833686|gb|CD973364.1|CD973364
EST:     GGACATAATACAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGGTTACACCATGCCTGACAGATTTAGGAGT
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATG-TTACACCATGCCTGACAGATTTAGGAGT
EST: gi|211517868|gb|FL476359.1|FL476359
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|211445567|gb|FL157339.1|FL157339
EST:     GACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCA-GGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|149000972|gb|EE038212.2|EE038212
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATCCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|32847430|gb|CD987111.1|CD987111
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGT
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGT
EST: gi|211445566|gb|FL157338.1|FL157338
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|32835473|gb|CD975151.1|CD975151
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|88756296|gb|DY540437.1|DY540437
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|76920399|gb|DV168154.1|DV168154
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATCCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|32834150|gb|CD973828.1|CD973828
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|60400106|gb|DN232913.1|DN232913
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|88757902|gb|DY542043.1|DY542043
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATCCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
EST: gi|71330189|gb|DR801853.1|DR801853
EST:     GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA
genomic: GGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTA

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: 259

GGGACAGGCGCCATGACCGTGATCGGGATAGGGATTATGACCGCTCCCGTGGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTACTGGCGGCGTCTGTTCAAGATATGGTTTGAGCTTGTGCTTCGTATCTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 169

GGGACAGGCGCCATGACCGTGATCGGGATAGGGATTATGACCGCTCCCGTGGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTACTGGCGGCGTCTGTTCAAGATATGGTTTGAGCTTGTGCTTCGTATCTTC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 248

GGGACAGGCGCCATGACCGTGATCGGGATAGGGATTATGACCGCTCCCGTGGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTACTGGCGGCGTCTGTTCAAGATATGGTTTGAGCTTGTGCTTCGTATCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

GGGACAGGCGCCATGACCGTGATCGGGATAGGGATTATGACCGCTCCCGTGGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... ccaatttcagGCGCCACGAGAGATACTAAATGTTACACCATGCCTGACAGATTTAGGAGTACTGGCGGCGTCTGTTCAAGATATGGTTTGAGCTTGTGCTTCGTATCTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACAGGCGCCATGACCGTGATCGGGATAGGGATTATGACCGCTCCCGTGGACATGATTCAAGGAGGAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctgaataatactcctcgtgtcacaaattataagacatctcccaaattataaggcgtcttagcttttctagatgtatttttttattatgtataca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA