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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgcttttcattattttcaagaacatcattttcttgataggttctggagagttttagtaggccctttgtaactcatgtgatggtagaagtgagttattgttgatacttttcctaaatccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATAAAATACTCCGGGAAAAGTTTGTGGAACTCTATGATACACCTATTCTGGA

Basic information

species Zea mays
transcript GRMZM2G381395_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381395_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os09g07120.1 (Oryza sativa), 3'ss of exon 17
gttggtgcttttcattattttcaagaacatcattttcttgataggttctggagagttttagtag-gccctttgtaactcatgtgatggtagaagtgagttattgttgatacttttcctaaatccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATAAAATACTCCGGGAAAAGTTTGTGGAACTCTATGATACACCTATTCTGGA
                            | || |||  |  |  |||||||  ||| ||  ||    || ||| |      |     | ||||||   ||| |    | | ||||   ||||| ||||||||||| |||||||| |||||||| |||||  ||||||||||||||||||| |||||||| || || ||||||||||||||||||||||| ||||| || ||
--------------------------gtaccagttt--tactgtgttctgggaagtgtttatattatcccttgcattaagcgcttaaggagaagtacattagtcgcaacatttttttaaaatc-aatgcagGAGTGCATGATTCGTATTGGACACATGCTTGTGATGTTGATACAATGAACAAAATACTACGAGAGAAGTTTGTGGAACTCTATGATACGCCTATCCTCGA
















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|76015991|gb|DT943161.1|DT943161
EST:     TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAG                         GAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
genomic: TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
EST: gi|91877942|gb|EB407899.1|EB407899
EST:     TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAG                         GAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
genomic: TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
EST: gi|83279316|gb|DV943324.1|DV943324
EST:     TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAG                         GAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
genomic: TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
EST: gi|6031435|gb|AW076337.1|AW076337
EST:     TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAG                         GAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
genomic: TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
EST: gi|74240731|gb|DT648645.1|DT648645
EST:     TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAG                         GAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
genomic: TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
EST: gi|31354501|gb|CD438858.1|CD438858
EST:     TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAG                         GAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA
genomic: TATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATA

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: 42 (upstream exon), 47 (downstream exon)
Score: 100

CAGAGGACAGCTTTCCCTCCAAACTTTGTGCATTCTCTTGATGGTTCTCATATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATAAAATACTCCGGGAAAAGTTTGTGGAACTCTATGATACACCTATTCTGGA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 48

CAGAGGACAGCTTTCCCTCCAAACTTTGTGCATTCTCTTGATGGTTCTCATATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATAAAATACTCCGGGAAAAGTTTGTGGAACTCTATGATACACCTATTCTGGA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 46

CAGAGGACAGCTTTCCCTCCAAACTTTGTGCATTCTCTTGATGGTTCTCATATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATAAAATACTCCGGGAAAAGTTTGTGGAACTCTATGATACACCTATTCTGGA


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 62

CAGAGGACAGCTTTCCCTCCAAACTTTGTGCATTCTCTTGATGGTTCTCATATGATGATGACTGCTGTTGCTTGCAAAAGGCAAGGTCTGAATTTTGCAGgttggtgctt ... tccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATAAAATACTCCGGGAAAAGTTTGTGGAACTCTATGATACACCTATTCTGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatgtgatggtagaagtgagttattgttgatacttttcctaaatccaatgcagGAGTTCATGATTCATATTGGACCCATGCCAGTGATGTTGATACAATGAATAAAATACTCCGGGAAAAGTTTGTGGAACTCTATGATACACCTATTCTGGA
                                      tcctaaa  putative branch site (score: 62)
                      ttattgtt  TA-rich tract