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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttttcaggtttgttaaatcatttgtcactgttggcttcttattgacagaaagttccctcttgtaactcag

Basic information

species Zea mays
transcript GRMZM2G077299_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 9
CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttttcaggtttgttaaatcat--ttgtcactgttggcttctt--attgacagaaagttccctcttgtaactcag
||| | ||||| |||||| |||  ||||||||||| |||||||||||||||  ||  ||  ||| ||| ||| |  |   ||| | || | || |  || ||||  ||  ||    ||  |  ||||
CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATGgtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactct---ttaaatatcag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G27460.3 (Glycine max), 5'ss of exon 9
CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaatt--gttttcaggtttgttaaatcatttgtcactgttggcttcttattgacagaaagttccctcttgtaactcag---------------------
|||||||||||| ||||||||| |||||| |||||||| || ||||||||||   | ||    | |||||| |  | | |   ||        || || | ||||| |   | ||  |   |||                      
CTTGCGGAGGACTTGGGTACTGCACCAATATGGGTATTTAATAATGgtaattttatgtttctctctgttaacttgtgtttgtttggaattgctttttttaaagaaaataatcactaatttttcaaaagctctctaaagaagctgcc
















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|32847594|gb|CD987275.1|CD987275
EST:     ACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: ACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|12045517|gb|BF727656.1|BF727656
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32846175|gb|CD985856.1|CD985856
EST:     ACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: ACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|6095297|gb|AW119964.1|AW119964
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|211082959|gb|FL420012.1|FL420012
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32865761|gb|CF005443.1|CF005443
EST:     GGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: GGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|78179997|gb|DV550370.1|DV550370
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|211043015|gb|FL421679.1|FL421679
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32846927|gb|CD986608.1|CD986608
EST:     ACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: ACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32835529|gb|CD975207.1|CD975207
EST:     GGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: GGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32846588|gb|CD986269.1|CD986269
EST:     GGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: GGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA

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), 38 (downstream exon)
Score: 46

CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 74

CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1040

CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttttcaggtttgttaaatcatttgtcactgttggcttcttattgacagaaagttccctcttgtaactcag

- -  GGAGGA