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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgtgggagactccggatagtgtagtctgttcctccctctttattgtgtttcagcagtgatcagtcacttattcatgttcatggtcttctttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC

Basic information

species Zea mays
transcript GRMZM5G802854_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 3
------acgtgggagactccggatagtgtagtctgttcctccctctttattgtgtttcagcagtgatcagtcacttattcatgttcatggtcttctttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC
          || ||| |  ||||     |    |||| |  |||| | ||||  ||||||  | | |      | | |    || ||  |  | || ||||  |||||| |||||||||||||||||| ||||||||| ||||||| |||||||||||||| 
tcttctcaaaggtagaatggggatttcaca--tagttctttactctct-ttgtccttcagcgcttagc--ctgttcactggcttttattcttat-ttcttttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT

upper sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 4
-------acgtgggagactccggatagtgtagtctgttcctccctctttattgtgtttcagcagtgatcagtcacttattcatgttcatggtcttctttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC
           || ||| |  ||||     |    |||  |      |  ||||  ||||||  | | | ||    |      | |  |  |||  ||  |||  |||||| |||||||||||||||||| ||||||||| ||||||| |||||||||||||| 
atcttctcaacggtagaatggggatttcaca--tagtttttttactctctttgtccttcagcgctaacctgttctctg-----gcttttattctatttcctttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT
















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|71756425|gb|DR954362.1|DR954362
EST:     TTGTATTGAAAACTCCCAGAAGCAGG                         TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAA
genomic: TTGTATTGAAAACTCCCAGAAGC-GGgtaagttcgg ... ttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAA
EST: gi|71434798|gb|DR815848.1|DR815848
EST:     TGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGG                         TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAA
genomic: TGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGGgtaagttcgg ... ttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAA
EST: gi|71433727|gb|DR814777.1|DR814777
EST:     TGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGG                         TATAAACCTTCTGT
genomic: TGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGGgtaagttcgg ... ttttttatagTATAAACCTTCTGT
EST: gi|211385471|gb|FL080437.1|FL080437
EST:     TGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGG                         TATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAA
genomic: TGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGGgtaagttcgg ... ttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAA

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), 45 (downstream exon)
Score: 18

GAGTGTGACACCATCGAGGCGACTAGTGCTGGGAAGTTGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGGgtaagttcgg ... ttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 56

GAGTGTGACACCATCGAGGCGACTAGTGCTGGGAAGTTGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGGgtaagttcgg ... ttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 36

GAGTGTGACACCATCGAGGCGACTAGTGCTGGGAAGTTGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGGgtaagttcgg ... ttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 73

GAGTGTGACACCATCGAGGCGACTAGTGCTGGGAAGTTGCGGCAGTTGAAACCCAACAAGTATTGTATTGAAAACTCCCAGAAGCGGgtaagttcgg ... ttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttcagcagtgatcagtcacttattcatgttcatggtcttctttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC
                                       tcttctttttttat  CT-rich tract
                                       tcttctttttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgtgggagactccggatagtgtagtctgttcctccctctttattgtgtttcagcagtgatcagtcacttattcatgttcatggtcttctttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC

- - - - - - - - - - - - - ctgttcc
- - - - - - - - - - - - - - - - - - - - - -ttgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - tcagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgg