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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT

Basic information

species Zea mays
transcript GRMZM5G840582_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 7
--------tgctagattctattgtgacactttgaatgtcattttctggatacc-tgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
        ||  ||||| || | ||| | |||| ||   |       |||||| |   | |  ||  ||  | ||| |       | |  ||||| | |||     ||||||||||| ||||||||||||||||||||||| | ||| ||||| |||||||| ||||| ||||||
tcatgtaatgtaagattttactttga-agtttggatagtagcac--agataccatttttctgtttgcttgtgatctaattacgttcctcatttca-tatga-----cagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT

upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 9
---tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttc-aatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
     ||| ||   |      ||     | |||||  |  |  ||   || |     |    | |     |||| |   | ||  | |  ||||    ||||||||||| |||||||||||||||||||||||||||  ||| ||||| |||||||| |  ||||| |||
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgcaacagctacactga----cgacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G04320.2 (Glycine max), 3'ss of exon 9
---tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttc-aatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
     ||| ||   |      ||     | |||||  |  |  ||   ||  ||||  ||         ||| | |   | ||  | |  ||||    ||||||||||| |||||||||||||||||||||||||||  ||| ||||| |||||||| |  ||||| |||
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgc-tatagcttcactga---tgatgcttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 3'ss of exon 9
----tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
    || | ||   |    |   |     | ||  |||   |  || |    | | | | ||| ||    ||  | ||       |    |  |||  |||||||| || |||||||| || |||||||||||||||  ||| ||||| ||||| || ||||| || |||
ttattgttggaaaatgaaattcaagcacaattgaaattccttctattc----aaacagtgtttaaacaattggtgctaatttggatcatcaaatgatgttgcagACTGTTGATGAGATTTATAAGGTTGCATCAATATCACTCAGTCCAAATGTCCCTGGGCAGATATTT

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|78112475|gb|DV530869.1|DV530869
EST:     AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
EST: gi|32850940|gb|CD990621.1|CD990621
EST:     AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
EST: gi|91054117|gb|EB164535.1|EB164535
EST:     CAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATATACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: CAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
EST: gi|7216933|gb|AW563070.1|AW563070
EST:     AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATATACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT

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), 43 (downstream exon)
Score: 39

GGAGGTTCAGCTTGTTTCTTTCCACACTGTGTCCAAAGGGTACTGGGGAGAGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

GGAGGTTCAGCTTGTTTCTTTCCACACTGTGTCCAAAGGGTACTGGGGAGAGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 3

GGAGGTTCAGCTTGTTTCTTTCCACACTGTGTCCAAAGGGTACTGGGGAGAGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

GGAGGTTCAGCTTGTTTCTTTCCACACTGTGTCCAAAGGGTACTGGGGAGAGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
                  gtctgac  putative branch site (score: 56)
     ataattttttaaggt  TA-rich tract