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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtccctttccaccacaccaaataattttaggaccctgacttttttttttttctccccggtcgtaacctatccagtaaccttactatggctgggctttcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT

Basic information

species Zea mays
transcript GRMZM2G061419_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 12
gtgagtgtccctttccaccacaccaaataattttaggaccctgacttttttttttttctccccggtcgtaacctatccagtaaccttactatggctgggctttcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT
|||||| |||||||| ||  |||| | | ||||        | | || | ||  |||  |     || | |  |     ||||| ||  | ||| ||  |||||||||| |||| ||||| |||||||||||||||||||| ||||| ||  |||| ||| || |||| ||||| |||||||||||||| |||||||| ||| ||||| || 
gtgagtttccctttcaac-gcacctacttattt---attatttagttatcttgcttttcctattatcatgattt-----gtaactttgttttggttgaactttcaattttagGTCTTCATAGCTGTGTTGGTAGACAACTTTCTCTACCCTATATCTGCATTCAGGTCTCATTTTTCCCAATCAATCAATTGGTCTGGTATCAGGTACCACC

upper sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA05G35860.1 (Glycine max), 3'ss of exon 11
gtgagtgtccctttccaccacaccaaataattttaggaccctgacttttttttttttctccccgg-tcgtaacctatccagtaaccttactatggctgggctttcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT
            |   |  |    |  |||| ||||||  || |   | |    | ||   |  | | |  |   |    ||||  |||      |||   | |      ||||||||||||||  || |||| || ||||| || ||||| || || ||| |||| || ||||| || ||||| ||||| |||||||| || |||||||| |
----------gatatgattatga-atgtaatattaggaaactaaggatgtgaaatatcaaacaagcttgctattaagttggtaaagtta--gaaactgacttcttttgaacagGTGTTCATCGCAATGCTGGTGGATAACTTTCTTTATCCTGTGTCTGCATTCCGCTCTCATTTTTCTCAATCTATCAATTGGTCTGGTATTCGGTACTATT

upper sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 12
gtgagtgtccctttccaccacaccaaataattttaggaccctgacttttttttttttctccccgg-tcgtaacctatccagtaaccttactatggctgggctttcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT
            |   |  |    |  ||||  || ||  || |   | |    | ||   |  | | |  |   |    ||||           |||   | |      ||||||||||||||  || |||| || ||||| || ||||| ||||| ||| |||| || ||||| || ||||| |||||||||||||| || |||||||| |
------------tatgattatga-atgtaatactatgaagctaagggtgtgaaatatcaaacaagcttgctattaagttggtaaaaagttagaaactgacttcttttgaacagGTGTTCATCGCAATGCTGGTGGATAACTTTCTTTATCCCGTATCGGCATTCCGCTCTCATTTTTCTCAATCTATCAACTGGTCTGGTATTCGGTACTATT

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|211068150|gb|FL154483.1|FL154483
EST:     TGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTC                         GTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATC
genomic: TGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTCgtgagtgtcc ... tcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATC
EST: gi|32928085|gb|CF032897.1|CF032897
EST:     TGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTC                         GTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATC
genomic: TGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTCgtgagtgtcc ... tcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATC

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: 47 (upstream exon), 49 (downstream exon)
Score: 253

CGTTTCAATGTGGAATTTGACTAAGGTGGAAATTCAACTGTGCAATATGCTGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTCgtgagtgtcc ... tcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 129

CGTTTCAATGTGGAATTTGACTAAGGTGGAAATTCAACTGTGCAATATGCTGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTCgtgagtgtcc ... tcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 73

CGTTTCAATGTGGAATTTGACTAAGGTGGAAATTCAACTGTGCAATATGCTGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTCgtgagtgtcc ... tcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 190

CGTTTCAATGTGGAATTTGACTAAGGTGGAAATTCAACTGTGCAATATGCTGTCTCCTGAAGGACCGAAAGTATCTCTTGATTCATACAACTGGGGGCTCgtgagtgtcc ... tcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccccggtcgtaacctatccagtaaccttactatggctgggctttcaatttcagGTGTTCATCGCTGTGTTGGTAGACAACTTCCTCTATCCAGTATCCGCAATCCGGTCGCATTTCTCCCAATCAATCAACTGGTCTGGCATCCGGTACTACT
                                          ctttc  CT-rich tract
                                           tttcaattt  TA-rich tract