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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaatcaaatggtattaagtatatttccatctcgataggtctgtgctgctttcatctaaccctattcattgcgttgttttcgtgactattcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC

Basic information

species Zea mays
transcript GRMZM2G066612_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066612_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g07690.1 (Oryza sativa), 3'ss of exon 4
---tcaaatcaaatggtattaagtatatttccatctcgataggtctgtgctgctttcatctaaccctattcattgcgttgttttcgtgactattcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC
    |  |    |  |||     |   ||  ||| || ||||||| | |    | |  |      ||    |||       | || ||  ||||| ||| ||||| |||||||| |||||||| ||||| ||||| ||||| || |||||| | || |||| | ||||| |||||||||| |||||||| |||||||||||||
agtcctgacattagagtagcttctcacttagcatatctataggtcagggtgcatgttgtaatgttcttccgatttaacaactctcttg--tattc-tctgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATAAAAAACGAGAAGCAGGTCGACAAGCTTGTGGGCGCCAACAAACCTGAGC

upper sequence: GRMZM2G066612_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G40970.1 (Glycine max), 3'ss of exon 4
-tcaaatcaa-atggtattaagtatatttccatctcgataggtctgtgctgctttcatctaaccctattcattgcgttgttttcgtgactattcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC
 |||| |||| |||   |  || | | |  ||  |    |    |||        ||| ||      |  |    | || |||| |  | ||   | |||||||||||||| ||||||||||||||   || || || || |||||||| || ||  | || || ||  | ||||| || || || || ||||| || || |
ttcaattcaacatgaactagaggacactatcacatattaaacattgtctgatgaccatgtagtttattgaacatgggtggtttcattgc-atatgt-tccagGACTTCAGCACTTCATGGGACATCAAAGCCACACCAACTTTCTTCTTTCTTAAAGATGGACAACAACTTGACAAACTTGTAGGAGCCAACAAGCCAGAAC
















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|44900360|gb|CK826905.1|CK826905
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
EST: gi|211449385|gb|FL478319.1|FL478319
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACGTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
EST: gi|84977611|gb|DW476033.1|DW476033
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
EST: gi|17932304|gb|BM269264.1|BM269264
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
EST: gi|18180492|gb|BM381702.1|BM381702
EST:     TCCTCAACTCATGTTCTTGGCAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: TCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
EST: gi|7162522|gb|AW520144.1|AW520144
EST:     AGACTTATCCTCAACTCATGTTCTTGCCAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
EST: gi|28984394|gb|BQ539056.2|BQ539056
EST:     AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATG                         GACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC
genomic: AGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 127

CTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 471

CTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

CTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 310

CTGGTGTGGGCCATGCCGTGTCATTGCTCCTGTCTATGCTGAAATGTCAAAGACTTATCCTCAACTCATGTTCTTGACAATAGACGTTGATGACCTGATGgtatttcaat ... tcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgctttcatctaaccctattcattgcgttgttttcgtgactattcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC
         atctaac  putative branch site (score: 310)
                                            ttcatctcc  putative PPT
                  tattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaatcaaatggtattaagtatatttccatctcgataggtctgtgctgctttcatctaaccctattcattgcgttgttttcgtgactattcatctccagGACTTCAGCTCTTCATGGGACATCCGTGCAACCCCGACATTCTTCTTCCTCAAGAACGGGCAGCAGATCGACAAGCTCGTGGGCGCGAACAAACCTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- -aatcaaa
- - - - - - - - - - - - - - - - - - - - - tgtgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttt