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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtacagtagcgtctacatcctctggccttgcatttgatgcacattctcttttctgccaacttaattattttttctctgaatatttttctctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG

Basic information

species Zea mays
transcript GRMZM2G460090_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 20
-------------------------------------------gcaagtacagtagcgtctacatcctctggccttgcatttgatgcacattctcttttctgccaacttaattattttttctctgaatatt--tttctctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG
                                             |  |   |   | | | ||||||| | ||         ||   ||| ||  |||  ||  ||  | ||||  |   ||  ||  |   ||| || |    | ||||||  || |||   || || || |||||||||||| ||||||||||||| || ||||| |||||||||||||||||||| ||| ||
gtaagtagatgtttgatgagatatcaaccacatgttccattgcagagatttcgcttcatgtgcatcctccgcccacaacacacatatgcatgcttatttgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG

upper sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 21
-------------------------------------------gcaagtacagtagcgtctacatcctctggccttgcatttgatgcacattctcttttctgccaacttaattattttttctctgaatatt--tttctctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG
                                             |  |   |   | | | ||||||||| ||         ||   ||| ||  ||   ||  ||  | ||||  |   ||  ||  |   ||| || |    | ||||||  || |||   || || || |||||||||||| ||||||||||||| || ||||| |||||||||||||||||||| ||| ||
gtaagtagatgtttgatgagatatcaaccacatgttccattgcagagatttcgcttcatgtgcatcctctgcccacaacacacatatgcatgcttattcgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG
















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|32933666|gb|CF038478.1|CF038478
EST:     GGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAG                         TAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGT
genomic: GGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGT
EST: gi|67016496|gb|CO445245.1|CO445245
EST:     GGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAG                         TAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGT
genomic: GGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGT
EST: gi|32846064|gb|CD985745.1|CD985745
EST:     GGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAG                         TAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGT
genomic: GGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGT
EST: gi|109179526|gb|EC380048.1|EC380048
EST:     GTTTNGCTGATGGTTCTGTCAGGATATATGAATGTTTGCTCTCCTGATAG                         CAGGCCTGTCT
genomic: GTTTTGCTGATGGTTCTGTCAGGATATATGA-TGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCT

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), 45 (downstream exon)
Score: 142

TCTGCATCTCAGGTCCGCTCTGGATACTTTGCTGCTGGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 58

TCTGCATCTCAGGTCCGCTCTGGATACTTTGCTGCTGGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 65

TCTGCATCTCAGGTCCGCTCTGGATACTTTGCTGCTGGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 104

TCTGCATCTCAGGTCCGCTCTGGATACTTTGCTGCTGGTTTTGCTGATGGTTCTGTCAGGATATATGATGTTTGCTCTCCTGATAGgcaagtacag ... ctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttttctgccaacttaattattttttctctgaatatttttctctctacacagTAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAG
              acttaat  putative branch site (score: 104)
                                    tatttttctctctac  putative PPT
             aacttaattatttttt  TA-rich tract