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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttgcatccatctctatttctatttttgttatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG

Basic information

species Zea mays
transcript GRMZM2G063909_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
gtacttttgcatccatctctatttctatttttgt-tatgttttggaagtacttg-------ttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
||| | |    ||||||  | |||  | || | | | |||||   ||  |||||       || ||| |||||||||  | ||||| ||| ||| |||||||||||||| || ||| ||||| |||||||||| ||||||
gtaatgtat--tccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 12
gtacttttgcatccatctctatttctatttttgttatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
||| ||     ||||||  | |||   ||| | ||   || |  |||   | ||||  |  | |  | || | ||||||||| ||| |||||||||||||| || ||  ||||| |||||||||| ||||||
gtaattcat--tccatccttgttttagtttctatttatttctaaaagacttggtttgatttctttttcctttcacctgtgttcttccagTGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
--------gtacttttgcatccatctctatttctatttttg---ttatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgt--tctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
         || || |      ||  | ||    || | |    || | || | | |  |  |     |      | || |      |    |||  || ||||||||||||||||||||| ||||| |||| ||||||||||| 
gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatcatataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA

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|211458206|gb|FL358448.1|FL358448
EST:     GACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGC                         TGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
genomic: GACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     GACGACCCCAGGATGCTGGAGCTGATGCGGCT-C------C-A-T-----                         TGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
genomic: GACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     GACGACCCCAGGATGCTGGAGCTGATGCGGCT-C------C-A-T-----                         TGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
genomic: GACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
EST: gi|78088374|gb|DV516767.1|DV516767
EST:     GACGACCTCAGGATGCTGGAGCTGATGCGGCTCCATGTAACATTTCACGC                         TGATCATGAAG
genomic: GACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAG

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: 46 (upstream exon), 43 (downstream exon)
Score: 127

CTGATGATTCTCTGGATTATGCGGCAAATTTATCACATATGCTTGGTTTTGACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 250

CTGATGATTCTCTGGATTATGCGGCAAATTTATCACATATGCTTGGTTTTGACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 31

CTGATGATTCTCTGGATTATGCGGCAAATTTATCACATATGCTTGGTTTTGACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 36

CTGATGATTCTCTGGATTATGCGGCAAATTTATCACATATGCTTGGTTTTGACGACCCCAGGATGCTGGAGCTGATGCGGCTCCATGTAACAATTCACGCgtacttttgc ... gttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
                                              ttgttct  CT-rich tract
                ttgtttttt  TA-rich tract