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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctactccaaattttcctactgagctttctgtttctgtttctaacttggtacttttgtagaaattctaactcttatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG

Basic information

species Zea mays
transcript GRMZM2G161969_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 15
gtaggctactccaaattttcctactgagctt-tctgtttctgtttctaacttggtacttttgtagaaattctaactcttatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG
               ||      |||| ||| ||| ||| | |    ||      || || ||    |   |    | | || | ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| |||||| || || ||||||||||| | ||||||||||
--------------gttagtaatctgaacttgtctatttatatgaaaaaaaaaaaacattggtttctagcttg-tacctgtgtttcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGGTGGCTCAAAGAGCAAGGGATAACAGCTTAAAACCTGAAGATTATGAG

upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 15
gtaggctactccaaattttcctactgagctttctgtttctgtttctaacttggt--acttttgtagaaa-----ttctaactctta--tgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG
                                  |||  |  |   ||||||    |  | ||||  ||     |||||||| ||   || ||||||||||||||||||| ||||||||||  ||||| ||||||||||||||||||||||||| |||||| || || || || |||||||  |||||||||
----------------------------------gttagtaatctaaacttgtctaatctgtgtaagaaaatgtttctaacttttgcttgttgcagGATGCAGACAAGAAAGGACTTGGTATGATTGCGGAGGAGGTGAAGCAGTTGGCTCAAAGAGCAAGGGATAACAGTTTGAAACCAGATGATTATGAG

upper sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaggctactccaaattttcctactgagctttctgtttctgtttctaacttggtacttttgtagaaattctaactcttatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG
   |  |  || ||||  |  |  | | | |  ||  | |    | |||||   | |  || |   ||   || |  |    | ||||| ||||||| |||||| ||    |||||||  || || ||   |   || ||||||||||||| ||| || |||||||| |||| ||||||||||
---gtgtgttcaaaatagtgtt--taaccct--tggctgtagcacaaacttcagattgctg-aattatataaatttcttgattccagGACGCAGACAGGAAGGGTCTGTCCACAATTGGAGAAGAAGTTCGGTTATTAGCTCAAAAAGCAAAAGAGAACAGCTTAAAGCCAGAAGATTATGAG

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|71329666|gb|DR801555.1|DR801555
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTG
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTG
EST: gi|26456540|gb|CA828123.1|CA828123
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGG
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGG
EST: gi|32932090|gb|CF036902.1|CF036902
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGT
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGT
EST: gi|32933945|gb|CF038757.1|CF038757
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACCAAGAAGGGACTTGGT
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGAC-AAGAAGGGACTTGGT
EST: gi|32930018|gb|CF034830.1|CF034830
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGTAC
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTAC
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTG
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTG
EST: gi|148935652|gb|EC879696.2|EC879696
EST:     GATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTG
genomic: GATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTG
EST: gi|32934396|gb|CF039208.1|CF039208
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGT
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGT
EST: gi|22472155|gb|BU036635.1|BU036635
EST:     TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGG                         GATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAG
genomic: TCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAG

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: 87

ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 103

ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

ATATCACAATGTGAACATCAACGTGGCTGTGCAGACTGAACACGGATTGTTTGTTCCAGTAATTAGGgtaggctact ... tatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttctgtttctaacttggtacttttgtagaaattctaactcttatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG
                                   ttctaac  putative branch site (score: 271)
                                         ctcttat  CT-rich tract
                                aaattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggctactccaaattttcctactgagctttctgtttctgtttctaacttggtacttttgtagaaattctaactcttatgctgcagGATGCAGACAAGAAGGGACTTGGTACAATTGCTGAGGAGGTGAAGCAGTTGGCTCAAAAAGCAAGAGACAATAGCTTAAAACCAGCAGATTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT