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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgtctgtctacttatttgtcacaaagcatgtttgcgtccagtttcgtgccatgcctgacatcatgtatattactttgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCATTCAGATCTCCGCTGGTTTCATGATCTTCTTCTCTATCCTAG

Basic information

species Zea mays
transcript GRMZM2G080387_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080387_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g28170.1 (Oryza sativa), 3'ss of exon 4
gtaagtgtgtctgtctacttatttgtcacaaagcatgtttgcgtccagtttcgtgccatg-------cctgacatcatgtatattactttgccta-acagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCATTCAGATCTCCGCTGGTTTCATGATCTTCTTCTCTATCCTAG
|||||||| | |   |  ||||     || |   |   |    |    | | |  | ||        ||| |||| ||| |||  | || ||| |  ||| |||||| | ||||| || ||||||||||||||||| ||||||||||| || |||||||||||||||||||||||||||||||| || ||||
gtaagtgt-tttccttctttatcgaaaactatttactctccgatatcctctagcactatcatgtattcctaacataatgcatacgatttcgccaacgcagAGAGAACATTGGTCTTCTTGGATCAACCAGGATTGGCAGCAGAAGAGTGATACAGATCTCCGCTGGTTTCATGATCTTCTTCTCCATTCTAG
















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|32940517|gb|CF045336.1|CF045336
EST:     TACTGCCAGCGGCTCTACTGTCTCTGT                         GGAGAACGTGGGTCTCCTATGATCAACCAGGATTGGTAGCAGAAGAGTCAT
genomic: TACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCAT
EST: gi|32945003|gb|CF049822.1|CF049822
EST:     ACTGCCAGCGGCTCTACTGTCTCTGT                         GGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCAT
genomic: ACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCAT
EST: gi|32941435|gb|CF046254.1|CF046254
EST:     TACTGCCAGCGGCTCTACTGTCTCTGT                         GGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCAT
genomic: TACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCAT
EST: gi|9731370|gb|BE510122.1|BE510122
EST:     CTGCTATTAGATGGCCTATTTGGTACTGCCAGCGGCTCTACTGTCTCTGT                         GGAGAACGTGGGTCTCCTANGATCAACCAGGATTGGTAGCAGAAGAGTCAT
genomic: CTGCTATTAGATGGCCTATTTGGTACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCAT

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), 47 (downstream exon)
Score: 72

GGAATCGGGCTGCTATTAGATGGCCTATTTGGTACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCATTCAGATCTCCGCTGGTTTCATGATCTTCTTCTCTATCCTAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 5

GGAATCGGGCTGCTATTAGATGGCCTATTTGGTACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCATTCAGATCTCCGCTGGTTTCATGATCTTCTTCTCTATCCTAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 2

GGAATCGGGCTGCTATTAGATGGCCTATTTGGTACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCATTCAGATCTCCGCTGGTTTCATGATCTTCTTCTCTATCCTAG


Block sizes: 33 (upstream exon), 47 (downstream exon)
Score: 4

GGAATCGGGCTGCTATTAGATGGCCTATTTGGTACTGCCAGCGGCTCTACTGTCTCTGTgtaagtgtgt ... tgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCATTCAGATCTCCGCTGGTTTCATGATCTTCTTCTCTATCCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcgtccagtttcgtgccatgcctgacatcatgtatattactttgcctaacagGGAGAACGTGGGTCTCCTAGGATCAACCAGGATTGGTAGCAGAAGAGTCATTCAGATCTCCGCTGGTTTCATGATCTTCTTCTCTATCCTAG
                      gcctgac  putative branch site (score: 4)
                                          ctttgcct  putative PPT
                                atgtatattacttt  TA-rich tract