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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catggatatacatgcattcatatatatctcctcgtttttgctactagctagctagtttcttgattgaacttactcttttttcgcacgcatgtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC

Basic information

species Zea mays
transcript GRMZM2G106560_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106560_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g29870.1 (Oryza sativa), 3'ss of exon 1
catggatatacatgcattcatatatatctcctcgtttttgctactagctagctagtttcttgat---tgaacttactcttttttcgcacgcatgtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC
 |   ||  | |   ||   |   | |||  |   |||  | |  |  | | || ||  | | |    |||  ||   ||  |           ||||||||| ||||||||| | ||||| |||||||||||||||||||||||||||||||||||||||||  ||||||||   ||||||||||| || ||||||||||| 
-agtaatgaaaaaaaatatttgc-tgtctaatttctttctcgatgaatttg-tatttcatcggtgcacgaatctaaaattaatgaatgaatgaatggatgcagGAGCTACTACCGGTGCACGCACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCGCGGGACGAGACGGTGGTGGTGACGACGTACGAGGGCACG

upper sequence: GRMZM2G106560_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G05880.1 (Glycine max), 3'ss of exon 1
--catggatatacatgc--attcatatatatctcctcgtttttgctactagctagctagtttcttgattgaacttactcttttttcgcacgcatgtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC
   |   | | | || |  |||| | |  ||||      || |  || |   ||  ||||    |   |||||| |    ||   |  | |        | ||| ||||||||||| ||||| || ||||||||||| ||||||||||| ||||| |||||  | |  ||||| || || ||||||||||| || |||||    
attaccaacaaaaattctcattcttcttcatctaggtagttatattaattaatatgtagtgaaatacatgaactga----ttaaacaaatgtgatgatttacagGAGCTACTACAGGTGCACGCATCAAGGGTGCAATGTGAAGAAGCAAGTGCAACGGCTAACCAAAGACGAAGGGGTAGTGGTGACCACTTATGAGGGAGTG

upper sequence: GRMZM2G106560_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G26400.1 (Glycine max), 3'ss of exon 1
catggatatacatgcattcatatatatctcctcgtttttgctactagctagctagtttcttgattgaacttactcttttttcgcacgcatgtg--gat--gcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC
  || |    | |    | || | | |        ||  |     || ||  |  |||  |  || ||   |    ||  |   ||  |||||  |||  |||| ||||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||  |  | |  ||||| || || ||||| ||||| || |||||    
-ttgaac---cgtaatcttatttttgttcatctaattaagtaggcagttatattattttgtagttaaatacatgaattaatgaaacaaatgtgttgatttgcagGAGCTACTACAGGTGCACGCATCAAGGGTGCAATGTGAAGAAGCAAGTGCAACGCTTAACCAAAGACGAAGGAGTAGTGGTAACCACTTATGAGGGAGTG

upper sequence: GRMZM2G106560_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0068g01770.t01 (Vitis vinifera), 3'ss of exon 1
-------catggatatacatgcattcatatatatctcctcgtttttgctactagctagctagtttcttgattgaacttactcttttttcgcacgcatgtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC
         ||     | ||    ||||||| |   |    || || | |||    | |  |    | || |  |  || | | | || |      ||||  |||||||||||||||||||| || || || || ||||| || |||||||||||||| || || || |  || ||  || | |||||||| || || || ||    
aatagtgtttgatagaatattttctcatatacaaaac----ttgttcccactcagaaacatggggatagactctaaatattttatattggt---tttgtgtttgcagAAGCTACTACAGATGTACCCATCAGGGATGCAATGTAAAGAAGCAGGTGCAACGCCTATCCAAAGATGAAAGCATTGTGGTGACTACTTATGAAGGGGTG

upper sequence: GRMZM2G106560_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0010g03930.t01 (Vitis vinifera), 3'ss of exon 1
---catggatatacatgcattcatatatatctcctcgtttttgctactagctagctagtttcttgattgaacttactcttttttcgcacgcatgtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC
       || | ||| |      ||  ||   ||| || ||    | | |  | | |     ||| |   ||  | |  |  ||    | |||||   ||||||||||| ||  | || ||||||||||||||||| |||||||||||||| || || || ||||  ||||| ||  | ||||| || || || || ||||  
aaaggctgaaaaacaagtccaattaagtactaccttgtcttgtagatttgagatccaaagatttggtgtgac--aatagtaatttaagctcatgttc-tgcagAAGCTATTATCGGTGTACACACCAAGGGTGCAATGTGAAGAAGCAGGTTCAACGCCTATCAAAAGACGAAGGAATCGTGGTCACAACTTATGAAGGCATG

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|18172584|gb|BM347972.1|BM347972
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|18165419|gb|BM335258.1|BM335258
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|28986869|gb|CB351350.1|CB351350
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|18166462|gb|BM336301.1|BM336301
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|18168920|gb|BM338760.1|BM338760
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|18168369|gb|BM338209.1|BM338209
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|18174198|gb|BM349586.1|BM349586
EST:     CCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTGCTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|18168596|gb|BM338436.1|BM338436
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
EST: gi|18174909|gb|BM350297.1|BM350297
EST:     CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACG                         AAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA
genomic: CGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCA

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 37

GGTTCGCCTTCCAGACGCGCAGCCAGGTCGACATCCTCGACGACGGCTACCGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

GGTTCGCCTTCCAGACGCGCAGCCAGGTCGACATCCTCGACGACGGCTACCGCTGGAGGAAGTACGGCCAGAAGGCCGTCAAGAACAACAACTTCCCACGgttagtagtt ... gtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctagctagtttcttgattgaacttactcttttttcgcacgcatgtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC
                     aacttac  putative branch site (score: 40)
                            tctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catggatatacatgcattcatatatatctcctcgtttttgctactagctagctagtttcttgattgaacttactcttttttcgcacgcatgtggatgcagAAGCTACTACAGATGCACACACCAAGGGTGCAACGTGAAGAAGCAGGTGCAGCGGCTGTCAAGGGACGAGGGCGTGGTGGTGACCACATACGAGGGCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG