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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagttacatctgcagcagtttgcatacacttgttgccccatcattgttccattttaccagaccctgacatctaacggtatttcttaaaaaaatacag

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T05 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 15
CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagttacatctgcagcagtttgcatacacttgttgccccatc-----------attgttccattttaccagac---cctgacatctaacggtatttcttaaaaaaatacag
|||||| ||||||||||  || ||||| ||||| |||||||||||||||||| |||||||| |||| ||| |||||||| ||  |||||  ||| | ||| |||| |  |      ||            ||| ||  |||| |||  |      |      |||   ||  | |  |||||||||||
CAATGTTTATGGCAATAAGCTAAATGGTTCTATTCCTGCTGGTTTCCAGAAGTTGGAGAGTCTGACTTACTTgtgagtaattgtatctgttgcattatgcttacagtaatcatttaattcactcggcgaaattattgtatttcacctaatgtttttcttgcttaaaaatacattt--aaaaaatacag
















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|149079907|gb|EE168913.2|EE168913
EST:     AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT                         AAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
genomic: AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
EST: gi|211105282|gb|FL067839.1|FL067839
EST:     AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT                         AAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
genomic: AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
EST: gi|211105280|gb|FL067837.1|FL067837
EST:     AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT                         AAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
genomic: AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT                         AAACCTTTCTTCAA
genomic: AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAA
EST: gi|148961185|gb|EE011900.2|EE011900
EST:     AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT                         AAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
genomic: AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
EST: gi|211105278|gb|FL067835.1|FL067835
EST:     AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCT                         AAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA
genomic: AATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 556

CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCACATAGTCAACTTGGACACACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCACATAGTCAACTTGGACACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420

CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagtt ... aaaaatacagAAACCTTTCTTCAAACAGTTTCAAAGGCCAGATTCCCTCTGAGCTTGGTCACATAGTCAACTTGGACACACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGTGTATGGCAATAGACTGAATGGCTCTATCCCTGCTGGTTTCCAGAAGCTGGAGAGTTTGACATACCTgtgagtagttacatctgcagcagtttgcatacacttgttgccccatcattgttccattttaccagaccctgacatctaacggtatttcttaaaaaaatacag

- - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA