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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgcatataatatctttatttgttagcagttgagcacatagttcatgctttgaaaaaattgtagccattgctaaatatggagatattcaactttttttacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT

Basic information

species Zea mays
transcript GRMZM2G461145_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g51540.1 (Oryza sativa), 3'ss of exon 7
--------gtcggtgcatataatatctttatttgttagcagttgagcacatagttcatgctttgaaaaaattgtagccattgc--taaatatggagatattcaactttttttacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT
         |   ||| |||||  |||||  | |||||||  ||   ||| |||||      |||||| ||| |    |      |||||   ||| | ||||| || | ||  || | |||||||| ||| | ||||||||||| |||  ||||||||| |||| |||||| ||| | ||||| ||||| ||| |||||||||| ||||||||  |||||
gtcagtgcttaactgcgtataacgtctttgctcgttagca--tgcaaacagagttc------tgaaaatattttttttaaaaaaataaatccagagtttttcaa-ttgtcttgttttacagGGATGAACAGGTTGACACTCAAGATGACTTGCAATGGGTTAGGAACAAGTTAAATGCCAGAGGGGCTAAACCTATTGATTTTGTCCAGACTGCTGCATCT
















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|211425655|gb|FL472964.1|FL472964
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|67037524|gb|CO464338.1|CO464338
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCAACACTCAAGAAGAACCGGCA-TGGGTCAGGGAGCA-G
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGA-CCGGCAATGGGTCAGG-AGCAAG
EST: gi|32834976|gb|CD974654.1|CD974654
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|211383644|gb|FL455006.1|FL455006
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|32863094|gb|CF002776.1|CF002776
EST:     GAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: GAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|83279349|gb|DV943357.1|DV943357
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|32930289|gb|CF035101.1|CF035101
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|32930245|gb|CF035057.1|CF035057
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|32833267|gb|CD972945.1|CD972945
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|17931921|gb|BM268881.1|BM268881
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCCACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
EST: gi|17931886|gb|BM268846.1|BM268846
EST:     CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCG                         GGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT
genomic: CGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTT

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: 141

ATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

ATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

ATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 60

ATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCACGGACACAGTTTACTATGCGgtcggtgcat ... tacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaattgtagccattgctaaatatggagatattcaactttttttacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT
                tgctaaa  putative branch site (score: 60)
                                      ctttttttactt  putative PPT
                              atattcaacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgcatataatatctttatttgttagcagttgagcacatagttcatgctttgaaaaaattgtagccattgctaaatatggagatattcaactttttttacttaaaagGGATGAGCAGCTCGACACTCAAGAAGACCGGCAATGGGTCAGGAGCAAGTTGAATACTAGAGGAGCTAAGCCTTTTGATTTTGTTCAGACTGCACCATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT