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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatccattctgttgtgctgattcccttaataagccgtggtgtggtcatttctaatgttactgaaatttctgctattgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA

Basic information

species Zea mays
transcript GRMZM2G350818_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G350818_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 12
gt-gaaatccattctgttgtgctgattcccttaat-aagccgtggtgtggtcatttctaatgtt-actgaaatttctgctattgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA
|| | |   |||||||   | || |||   ||  | |||| |||||||| |  ||     | ||   |||||| ||| ||  ||||| ||||| ||||||| || ||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| |||||||
gtagcagaacattctgcattcctaatttgtttctttaagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA

upper sequence: GRMZM2G350818_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 15
-gtgaaatccattctgttg-tgctgattcccttaataagccgtggtgtggtcatttctaatgttactgaa-atttctgctattgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA
    | | |||   |||   |           | |  | |  |||   | |    || ||| | |||    |||||||  ||  |  ||| |  |||||||||||||    || ||||||||  |||||||||||||| ||||||||   |||||||| || |||||||||||||||||||| |  ||  
gtccataaccaacttgtgaatttcagggatactcaccaactttggaacgttacaatcaaatttaactttgcatttctgtgatc-tttcagATTATGGAAACAAACAGAAGTGAGGAATCTCAGAGTCATGTGCACAGGTTGTATTTCCATGGCCCAAATACATTCAGTGAACCTTGGCATCTACTTCATT

upper sequence: GRMZM2G350818_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 16
-------gtgaaatccattctgttgtgctgattcccttaataagccgtggtgtggtcatttctaatgttactgaaatttctgctattgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA
          || | | || ||   | | |     || | ||  |  |||  || |    || ||| | |||   | || ||  |   |  ||| |  |||||||||||||    || |||||||   |||||||||||||| ||||||||  ||||||||| || |||||||||||||||||||| || ||  
gtccataactaacttccttgtgaatttcagggatactcattac-ctttggaatgttaccatcaaatttaactttgaattttgtgagc-tttcagATTATGGAAACAAACAGAAGTGAGGAATCTCCGAGTCATGTGCACAGGTTGTATTTCCAGGGCCCAAATACATTCAGTGAACCTTGGCATCTACCTCATT

upper sequence: GRMZM2G350818_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
-gtgaaatccattctgttgtgctgattcc-cttaataagccgtggtgtggtcatt----tctaatgtta--ctgaaatttctgctattgt-----ggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA
 || |  |   |||    |   | ||||  |  ||||| |||        || ||    |  | ||||   |||   ||| |  | || |     | ||||| ||||||||||| || || ||  |||||||  |||||||||| || |||||||| ||||| || || || ||||||||||| ||||||||| ||||||
agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacactccttatattacagtgttgtgctgctgtttataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA

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|33770943|gb|CF273237.1|CF273237
EST:     ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTTGAATCACTGAATGAG                         GTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATG
genomic: AGAGCTCCCAAATTGATCACTCTTTTCCCTTCCTTGAATCACTGAATGAGgtgaaatcca ... attgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATG




















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: 45 (upstream exon), 49 (downstream exon)
Score: 175

GATGAAGTTTGTTGGTACTGATGAGTTGCCTGGACCAGCACCAACTCAACAGAGCTCCCAAATTGATCACTCTTTTCCCTTCCTTGAATCACTGAATGAGgtgaaatcca ... attgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 115

GATGAAGTTTGTTGGTACTGATGAGTTGCCTGGACCAGCACCAACTCAACAGAGCTCCCAAATTGATCACTCTTTTCCCTTCCTTGAATCACTGAATGAGgtgaaatcca ... attgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

GATGAAGTTTGTTGGTACTGATGAGTTGCCTGGACCAGCACCAACTCAACAGAGCTCCCAAATTGATCACTCTTTTCCCTTCCTTGAATCACTGAATGAGgtgaaatcca ... attgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

GATGAAGTTTGTTGGTACTGATGAGTTGCCTGGACCAGCACCAACTCAACAGAGCTCCCAAATTGATCACTCTTTTCCCTTCCTTGAATCACTGAATGAGgtgaaatcca ... attgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagccgtggtgtggtcatttctaatgttactgaaatttctgctattgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA
                    ttctaat  putative branch site (score: 249)
                  atttctaat  TA-rich tract