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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaatcctcagcacatgagctctcttcttactatacaggtcgcgtggactctgaatagctgatggtctgtttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG

Basic information

species Zea mays
transcript GRMZM5G825090_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804772_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g44400.1 (Oryza sativa), 3'ss of exon 9
gtctgaatcctcagcacatgagctctctt---cttactat-----acaggtcgcg--tggactctgaa--tagctgatggtctgtttttcg-cagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG
|||||||||||| ||| ||     |  ||    || |  |        | |  |     ||  | |||  |  | | ||     ||| ||  ||||||||||| ||||||||| ||||||||||||| ||||| || || || ||||||||  ||||||||||
gtctgaatcctctgcatattgatacgtttgcatttgccgtttcctgtggcttactgccagatccagaatctgaccggtgcatgctttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG
















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|33467263|gb|CF244312.1|CF244312
EST:     ACATTGCTTCAAAAGTCCCCCCGCAGCCCATAGAGATATGGGCATGTGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAGgtctgaatcc ... tttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
EST: gi|211011083|gb|FL375748.1|FL375748
EST:     ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAG                         GGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAGgtctgaatcc ... tttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
EST: gi|67011570|gb|CO440319.1|CO440319
EST:     ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAG                         GGATCTTCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG
genomic: ACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAGgtctgaatcc ... tttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTG

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: 38 (upstream exon), 12 (downstream exon)
Score: 1

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAGgtctgaatcc ... tttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG


Block sizes: 49 (upstream exon), 12 (downstream exon)
Score: 2

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAGgtctgaatcc ... tttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG


Block sizes: 42 (upstream exon), 32 (downstream exon)
Score: 2

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAGgtctgaatcc ... tttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG


Block sizes: 32 (upstream exon), 18 (downstream exon)
Score: 1

GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATGTGAGgtctgaatcc ... tttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttactatacaggtcgcgtggactctgaatagctgatggtctgtttttcgcagGGATCTCCCTTCTGTAAATTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG
                                         tctgtttttc  CT-rich tract
                                           tgttttt  TA-rich tract