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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtccaactgttggttttggttgcctttaatgtatatatagttccgcacatctctaatactgtttcctttatcatgctgcaattcacttgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT

Basic information

species Zea mays
transcript GRMZM5G821024_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821024_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06170.2 (Oryza sativa), 3'ss of exon 2
---cttgtccaactgttggttttggttgcctttaatgtatatatagttccgcacatctctaatactgtttcctttatcatgctgcaattcacttgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT
    |  || | ||  |||||||       | |||| ||| | | | ||  |||||  |||||  | |  ||||| ||||  || |||| |||| |  | ||||||||||| |||||  ||||  |||||||||| ||||| || |||||| ||||| |||||||||||||||||||||| |||||||               
tgaatgttctatcttatggttttttgattttctaat-tatcttttgctc-acacattcctaattttataccctttttcatcttggaatttacttatggt-cagAGGGACACGTCTGGCCTAACTGCTGAGAACAGAGAGCTCAAACTCCGGTTGCAGTCCATGGAAGAACAAGCTAAACTTCGAGATG---------------
















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|93282762|gb|EB675026.1|EB675026
EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTG
genomic: CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTG
EST: gi|76017161|gb|DT944331.1|DT944331
EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGG
genomic: CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGG
EST: gi|32797919|gb|CD950155.1|CD950155
EST:     GCTGCAGACAGAGGCCACCACACCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGG
genomic: GCTGCAGACAGAGGCCACCACAC-TTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGG
EST: gi|71427972|gb|DR809022.1|DR809022
EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTC
genomic: CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTC
EST: gi|76289897|gb|DV029465.1|DV029465
EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCT
genomic: CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCT
EST: gi|78121825|gb|DV540209.1|DV540209
EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTTCTGGTT-AACCACTGAGAACAGGGAGC
genomic: CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCT-CTGGTTTAACCACTGAGAACAGGGAGC
EST: gi|74233756|gb|DT641670.1|DT641670
EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTG
genomic: CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTG
EST: gi|76921491|gb|DV168604.1|DV168604
EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTG-TTTAACCACTGAGAACAGGGAGCT
genomic: CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCT

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), 47 (downstream exon)
Score: 31

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 33

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 33

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcacatctctaatactgtttcctttatcatgctgcaattcacttgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT
        ctctaat  putative branch site (score: 33)
                                       ttcactt  putative PPT
                        tttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtccaactgttggttttggttgcctttaatgtatatatagttccgcacatctctaatactgtttcctttatcatgctgcaattcacttgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGGTACGTAGTCTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - tgttggt
- - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - - - - - -gcacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctgc