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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgttttctgcccagttcctgtgaaatactgtacatcatatgtctttcttcactacggttcaaaccttctaacttatatttctcctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG

Basic information

species Zea mays
transcript GRMZM2G105539_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 3'ss of exon 7
gtaggtgttttctgcccagttcctgtgaaatactgtacatcatatgtctttcttcactacgg-ttcaaaccttctaacttatatttctcctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG
||| || ||| |     | ||||| |||| |  ||          || ||||||||| | |  || |||||||  || || |  |||||| ||| ||||| |||||||| ||||| || ||||||||||||||| ||||  |||| ||||| || ||||| |||||||| || |||||||| ||||| || ||||| 
gtaagtatttgcc-taaaattcctctgaact--tg----------gtgtttcttcaccatgtctttaaacctttgaatttgttattctcccccttaagGCAAACAAATTGGAGCAGCTGAGAGAAAGGATGGTCCAAGTGCGAGAACTTTTTCGTGACACAGAATCAACTGAATTTATAATTGTGACTATTCCAACA

upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaggtgttttctgcccagttcctgtgaaatactgtacatcatatgtctttcttcactacggttcaaaccttctaacttatatttctcctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG
                 |||   |||  | |     | ||  |||  || | |||| |  |||| |||  ||||   ||||   | ||     | ||||  ||||||| ||  |||| |||||||||||||| |||||  | ||||||||||| ||||| || |||||||| ||  | || || || |||||||||
--------------gtaagtctttgtacattggctgatatagtattcctgttttcatt-tggttaaaattttct---ttatggatgtc-----acagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG
















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|87153613|gb|DY398402.1|DY398402
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCA                         GCGAACAAATTAGAGCAACCCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
EST: gi|148958813|gb|EC905077.2|EC905077
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAG
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAG
EST: gi|5846791|gb|AI999874.1|AI999874
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGGAGGATGCA                         GCGAACCAAATTAGAGCAACTCAGNAGAAAGGATGGTCAAAGTAAGAGAGC
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAAC-AAATTAGAGCAACTCAG-AGAAAGGATGGTCAAAGTAAGAGAGC
EST: gi|6973389|gb|AW438083.1|AW438083
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGCCCAACAGGAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
EST: gi|6031284|gb|AW076291.1|AW076291
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGGAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
EST: gi|5296253|gb|AI782933.1|AI782933
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGGAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
EST: gi|211363054|gb|FL031142.1|FL031142
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
EST: gi|18385084|gb|BM418283.1|BM418283
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
EST: gi|87152689|gb|DY397478.1|DY397478
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
EST: gi|22489513|gb|BU049436.1|BU049436
EST:     CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCA                         GCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT
genomic: CATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTT

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), 48 (downstream exon)
Score: 99

CTGAGGAGTAAGATTGCTTCTGCAACATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

CTGAGGAGTAAGATTGCTTCTGCAACATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 67

CTGAGGAGTAAGATTGCTTCTGCAACATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 95

CTGAGGAGTAAGATTGCTTCTGCAACATCAGCTATTAAATCAGTATTTGGACAAGAGGTCCAACAGCAGGATGCAgtaggtgttt ... cctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtctttcttcactacggttcaaaccttctaacttatatttctcctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG
                            ttctaac  putative branch site (score: 95)
                                  cttatatttctcctcc  CT-rich tract
                            ttctaacttatattt  TA-rich tract