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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtttcactagtgcacaaatcctacagcgtttatgcaaaacaacaacgacgacgaaaatctccccgaccaaatgatactacgatttgcagGCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGACCGCCTGACGTTCTTGGCCTCCGCCGCTGGGAAG

Basic information

species Zea mays
transcript GRMZM2G144407_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144407_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 9
gtgagtgtttcactagtgcacaaatcctacagcgtttatgcaaaacaacaacgacgacgaaaatctccccgac--caaatgatactacgatttgcagGCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGACCGCCTGACGTTCTTGGCCTCCGCCGCTGGGAAG
|||||  ||||| |||| || | || ||||    |  |       ||||   |  ||| |   | || | ||   | ||||    || | |||||||  | || ||||||| |||||||| |||||||||||| || | || ||||| || |||| ||||||||||||  | ||||| |||
gtgagcatttcagtagttca-atatactacgagttcca-------caac--tgttgactattgtttctctgatttctaatgtgtgtatgttttgcagAGTGCTTTGGTTGCATTAGCTACTTATGCTTCAGATTCTACTGAAGCTGATCGTCTGAGGTTCTTGGCCTCTCCTGCTGGAAAG
















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|71319099|gb|DR796311.1|DR796311
EST:     TGAGGAATGCGCTCGCTAGATACGCCGACCTTCTGAATTCCCCGAAGAAG                         GCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGAC
genomic: TGAGGAATGCGCTCGCTAGATACGCCGACCTTCTGAATTCCCCGAAGAAGgtgagtgttt ... cgatttgcagGCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGAC




















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 3 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 41

CGCAGACAGAGACGACGGCAGTCCTCCTCCATTCCCGTCCCCAACCACACTGAGGAATGCGCTCGCTAGATACGCCGACCTTCTGAATTCCCCGAAGAAGgtgagtgttt ... cgatttgcagGCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGACCGCCTGACGTTCTTGGCCTCCGCCGCTGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

CGCAGACAGAGACGACGGCAGTCCTCCTCCATTCCCGTCCCCAACCACACTGAGGAATGCGCTCGCTAGATACGCCGACCTTCTGAATTCCCCGAAGAAGgtgagtgttt ... cgatttgcagGCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGACCGCCTGACGTTCTTGGCCTCCGCCGCTGGGAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 12

CGCAGACAGAGACGACGGCAGTCCTCCTCCATTCCCGTCCCCAACCACACTGAGGAATGCGCTCGCTAGATACGCCGACCTTCTGAATTCCCCGAAGAAGgtgagtgttt ... cgatttgcagGCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGACCGCCTGACGTTCTTGGCCTCCGCCGCTGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaacaacaacgacgacgaaaatctccccgaccaaatgatactacgatttgcagGCTTCTCTGGTTGCGTTAGCTACGTATGCTTCAGATCCTGCCGAGGCTGACCGCCTGACGTTCTTGGCCTCCGCCGCTGGGAAG
                                  aaatgata  TA-rich tract