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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatctgtcagaaactttacaccttgcttcacttgccaagtagaatgtgaacttctgtgtcttctatgtagtccgagatcaaagtaacatatgtgctgatttgcaactccgactttgattttgttgaaatttaactagtggtttgctccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG

Basic information

species Zea mays
transcript GRMZM2G412911_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412911_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g18730.1 (Oryza sativa), 3'ss of exon 12
gtatgcatctgtcagaaactttacaccttgcttcacttgccaagtagaatgtgaacttctgtgtcttctatgtagtccgagatcaaagtaacatatgtgctgatttgcaact-----ccgactttgattttgttgaaatttaactagtggtttgctccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG
||||| |||| | | | | ||| |           ||||||        |||| | || | | ||||  |||||||||||| ||||||||   || |  ||||  ||||| |     | |||||||||||| |||||| ||||| |||| |||||| |||||||||||| | ||||||||||| ||||||  | |||||
gtatgtatctcttatagaattttc-----------cttgccg-------tgtgtattttttt-tctttaatgtagtccgagttcaaagtag--tacgaactgacctgcaaattaaggctgactttgattttcttgaaacttaaccagtg-tttgctacttttgtagTTTAAATGCTCAAGTGGTATCAGTCCTGTGGAG
















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|26457309|gb|CA828892.1|CA828892
EST:     AGGTCACAACTAAGAATATTGGTACACTGGAGGCTTCGTATACCTTGACA                         TTTCACTGCTCAAGTGGCATCAGTTTTATGGAG
genomic: AGGTCACAACTAAGAATATTGGTACACTGGAGGCTTCGTATACCTTGACAgtatgcatct ... ccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG




















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), 33 (downstream exon)
Score: 130

AGACATTAGTGTTCCAGCATTTGAAGTCTTAAGTCAATATGGTACTGCAAAGGTCACAACTAAGAATATTGGTACACTGGAGGCTTCGTATACCTTGACAgtatgcatct ... ccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 54

AGACATTAGTGTTCCAGCATTTGAAGTCTTAAGTCAATATGGTACTGCAAAGGTCACAACTAAGAATATTGGTACACTGGAGGCTTCGTATACCTTGACAgtatgcatct ... ccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 40

AGACATTAGTGTTCCAGCATTTGAAGTCTTAAGTCAATATGGTACTGCAAAGGTCACAACTAAGAATATTGGTACACTGGAGGCTTCGTATACCTTGACAgtatgcatct ... ccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 53

AGACATTAGTGTTCCAGCATTTGAAGTCTTAAGTCAATATGGTACTGCAAAGGTCACAACTAAGAATATTGGTACACTGGAGGCTTCGTATACCTTGACAgtatgcatct ... ccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaactccgactttgattttgttgaaatttaactagtggtttgctccttttgtagTTTCACTGCTCAAGTGGCATCAGTTTTATGGAG
                          atttaac  putative branch site (score: 53)
                                       tttgctccttttgt  putative PPT
           tttgattttgttgaaa  TA-rich tract