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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagtttttccaaacaccaattggattattctttccttatttaattcttgttctgttccaattttgttcttctgctgcattctgaatgagactgatgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAGCCATATAGGCTGACACGGCGATGTGAAGTGACTGCAATTCTTATTCTGT

Basic information

species Zea mays
transcript GRMZM2G017845_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 9
gtgagagtttttccaaacaccaattggattattctttcctta--tttaattcttgttctgttccaattttgttct-tctgctgcattctgaatgag-------actgatgtt------ttcagATACTG---AGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAGCCATATAGGCTGACACGGCGATGTGAAGTGACTGCAATTCTTATTCTGT
||||||  | |||  | ||  |  || ||   ||||| | ||  || ||||||  |||  ||  | |  | | || | | |||  |||||| ||||       | | || ||      || ||||| ||   |||||||||||||||||||| ||| |||||| ||||||||| |||||||||||| |||| || ||||||||||||||||||||||| ||||   
gtgagaactattctgagcatgagatgaatggatcttttcataatttaaattctatttcaattgtattggtctgctgtgttctgacttctgactgagttccagcatttatttttaatattttagATATTGAGGAGACCAAGAATGGCTGGAAATAAAGTTATGGAAATGATAACGGAGCCATATAGGTTGACTCGTCGATGTGAAGTGACTGCAATTCTCATTC---
















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|110191747|gb|EC873645.1|EC873645
EST:     AGAACAGACTGTTAGCACG                         ATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAG
genomic: AGAACAGACTGTTAGCACGgtgagagttt ... atgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAG
EST: gi|78116577|gb|DV534964.1|DV534964
EST:     GAAACAAGAGGACTATGCTTATCAGAAGAACAGACTGTTAGCACG                         ATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAG
genomic: GAAACAAGAGGACTATGCTTATCAGAAGAACAGACTGTTAGCACGgtgagagttt ... atgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAG

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), 45 (downstream exon)
Score: 49

GGTCACCACCATCTTCCTGAAACAAGAGGACTATGCTTATCAGAAGAACAGACTGTTAGCACGgtgagagttt ... atgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAGCCATATAGGCTGACACGGCGATGTGAAGTGACTGCAATTCTTATTCTGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 139

GGTCACCACCATCTTCCTGAAACAAGAGGACTATGCTTATCAGAAGAACAGACTGTTAGCACGgtgagagttt ... atgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAGCCATATAGGCTGACACGGCGATGTGAAGTGACTGCAATTCTTATTCTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

GGTCACCACCATCTTCCTGAAACAAGAGGACTATGCTTATCAGAAGAACAGACTGTTAGCACGgtgagagttt ... atgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAGCCATATAGGCTGACACGGCGATGTGAAGTGACTGCAATTCTTATTCTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

GGTCACCACCATCTTCCTGAAACAAGAGGACTATGCTTATCAGAAGAACAGACTGTTAGCACGgtgagagttt ... atgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAGCCATATAGGCTGACACGGCGATGTGAAGTGACTGCAATTCTTATTCTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgttccaattttgttcttctgctgcattctgaatgagactgatgttttcagATACTGAGACCAAGAATGGCTGGAAACAAAATTATGGGAATGATAACAGAGCCATATAGGCTGACACGGCGATGTGAAGTGACTGCAATTCTTATTCTGT
                                        gactgat  putative branch site (score: 112)
                                              tgttttc  CT-rich tract
          aattttgtt  TA-rich tract