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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaatttggtgtcatcgttatgaaaagttgtttgagctattgattaatgattattttttctggtgacctttctatgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA

Basic information

species Zea mays
transcript GRMZM2G138125_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138125_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g59624.2 (Oryza sativa), 3'ss of exon 8
gtttgaatttggtgtcatcgttatgaaaagttgtttgagctattgattaatgattatttt--ttctggtgacctt----tctatgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA
||    ||    |  ||  | |   |||   || ||  | ||||| ||||     || ||  |  | ||    ||    | | || ||||||||| || |||||||||||||||| || ||||| || ||||||| | || ||||       |  ||||| ||||| |||||||| 
gtacagatcattttccactgatgcaaaactctggttttgttattggttaactgccatcttaatattagtccttttttattttttggatgcagAGGCAATTATATGAAGCTTTTCTTAACAGTGAACTAGTTCATTCATCAATGCAA------GGGTCACCCTTGGCCGCAATCACG
















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|211389135|gb|FL355235.1|FL355235
EST:     TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAG                         AGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG
genomic: TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG
EST: gi|67035224|gb|CO463757.1|CO463757
EST:     TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAG                         AGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG
genomic: TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG
EST: gi|211102981|gb|FL307628.1|FL307628
EST:     TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAG                         AGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG
genomic: TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG
EST: gi|32931646|gb|CF036458.1|CF036458
EST:     TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAG                         AGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG
genomic: TAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTG

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: 145

CCTGAAAAGTGAAGTTGTCTTTGATACTGGTGCATCAGAAGAAAAAACATTAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA


Block sizes: 33 (upstream exon), 45 (downstream exon)
Score: 34

CCTGAAAAGTGAAGTTGTCTTTGATACTGGTGCATCAGAAGAAAAAACATTAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 20

CCTGAAAAGTGAAGTTGTCTTTGATACTGGTGCATCAGAAGAAAAAACATTAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 64

CCTGAAAAGTGAAGTTGTCTTTGATACTGGTGCATCAGAAGAAAAAACATTAGCCAAGAAGAATGAGCTAATTGTCTGGCTGAAGTTAACACCATGCCAGgtttgaattt ... atgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgagctattgattaatgattattttttctggtgacctttctatgcatgcagAGGAAACTATATGAAGCTTTTCTAAATAGTGAGCTGGTTCATTTAGCATTGCAGCCAAAGGCATCACCGTTGGCTGCAATCACA
             gattaat  putative branch site (score: 64)
                                      cctttctat  putative PPT
         tattgattaatgatta  TA-rich tract