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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatattccaaaccatggatttgtttttctgattgctggtttgatcaattgctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG

Basic information

species Zea mays
transcript GRMZM2G001713_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G899123_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 8
gtttgtatattccaaaccatggatttgtttttctgattgctggtttgatcaattgc-tcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG
         ||   ||   | | ||   |||||||    | | |||  ||||||   ||||  |    ||   |||  |||||| ||   || |||| ||||||||||| ||| | || ||||| ||||||||||||||||| ||||||||||| |  |||||||| ||
--------gtttgtaat--ttgcttcaattttctggaaacagcttttgtcaattatatctttga----tgaattaaaacaactttctg--ggattatgttgcagACACAGCCATCAAAAATCTGCTCTCAGGTTGGTCTGTGTACTTTTGATGGGAAGCATGGTGTTAG
















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|211224723|gb|FL222441.1|FL222441
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAACGAAGATCTGTTCCCAGGTTGGTCTGTGCACYTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|31361595|gb|CD445952.1|CD445952
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAACGAAGATCTGTTCCCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|211222666|gb|FL222431.1|FL222431
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAACGAAGATCTGTTCCCAGGTTGGTCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGC
EST: gi|211224720|gb|FL222438.1|FL222438
EST:     CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAG                         ACACAACCAACGAAGATCTGTTAC-CAGGTTGGTCTGTGCACTTTTGATGG
genomic: CTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTT-CTCAGGTTGGTCTGTGCACTTTTGATGG

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: 49 (upstream exon), 49 (downstream exon)
Score: 780

AATCAATGAAAAGATTGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1390

AATCAATGAAAAGATTGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 864

AATCAATGAAAAGATTGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 860

AATCAATGAAAAGATTGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAGCAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattgctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG
                     cggtaac  putative branch site (score: 860)
                                            ttatttt  putative PPT
                                            ttatttt  TA-rich tract