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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTGCCGTTCTCGGATGCACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgataccgtgatatataattgtgtttgctattatgccaataattgcgatagcaccacctgctcattttcttctcacatcgaatacttctggtta...

Basic information

species Zea mays
transcript AC209858.4_FGT002
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209858.4_FGT002 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g05720.1 (Oryza sativa), 5'ss of exon 9
GCATTGCCGTTCTCGGATGCACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgataccgtgatatataattgtgtttgcta-ttatgccaataattgcgatagcaccacctgctcattttcttctcacatcgaatacttc--tggtta
 ||||||| ||||| |||||||| ||| ||||||||||||| |||||||||||| |||||||||  ||||||||||| ||  ||  |  ||   | | | | ||| ||||| || ||| ||  ||    |   |  ||   |   ||  ||   | |  ||| |  | |  |
TCATTGCCATTCTCAGATGCACTTAAGATCATGTCTTACTTAAAGGAGTGGTCTATGGTTCCTTTGAAGgtaaaatgcta--gtacttcattgctctctatactagttatgtca-taaatgtaatttacctgtcaactttctcagtttccaatcctatgactgcaatagaca
















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|32833350|gb|CD973028.1|CD973028
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|32937153|gb|CF041972.1|CF041972
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|32932056|gb|CF036868.1|CF036868
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|32835694|gb|CD975372.1|CD975372
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|32835920|gb|CD975598.1|CD975598
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|32832909|gb|CD972587.1|CD972587
EST:     CGCTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|211417128|gb|FL448753.1|FL448753
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|78084366|gb|DV512759.1|DV512759
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|211057077|gb|FL049064.1|FL049064
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGRTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|32833351|gb|CD973029.1|CD973029
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
EST: gi|78084367|gb|DV512760.1|DV512760
EST:     CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAG                         GTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT
genomic: CACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAAT

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), 49 (downstream exon)
Score: 105

GCATTGCCGTTCTCGGATGCACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAATCAATTAACTGCCACGCCAGCTGCAAGATCCTTGTTGACAGAACTGAAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 43

GCATTGCCGTTCTCGGATGCACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAATCAATTAACTGCCACGCCAGCTGCAAGATCCTTGTTGACAGAACTGAAGG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 68

GCATTGCCGTTCTCGGATGCACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAATCAATTAACTGCCACGCCAGCTGCAAGATCCTTGTTGACAGAACTGAAGG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 26

GCATTGCCGTTCTCGGATGCACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgat ... aaccttgcagGTTGAGCTTGTTTGTAGGGTTTGCTTAGTGCTCCTTCAGACACATCACAATCAATTAACTGCCACGCCAGCTGCAAGATCCTTGTTGACAGAACTGAAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTGCCGTTCTCGGATGCACTAAAGCTCATGTCTTACTTGAAGGAGTGGTCTTTGGTTCCTTCAAAGgtaaaatgataccgtgatatataattgtgtttgctattatgccaataattgcgatagcaccacctgctcattttcttctcacatcgaatacttctggtta

- - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - AAGGAG