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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcaccattcagctagtgacatgactacttcttgttctgtttatgtgattctgatttgttaatgtttatttgctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g16970.3 (Oryza sativa), 3'ss of exon 7
----gtgatcaccat--tcagctagtgacatgactacttc--ttgttctgtttatgtgattct-gatttgttaatgtttatttgctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT
     || |     |   | ||     |  |  || |||    |  | | | ||| || || | ||||| |   | ||  |||| | |  ||||||| ||||   | || || ||||| ||| |||| ||||||||||| ||||||||||||||||| | || |||||||||||| | ||||||||| |||||
gtatatggttcatgtaacctgcccactatctctcttctttgactcctttctgtatttggttatcgatttttcttttttcttttgttctgtcagATTTCACTGCCTCTGGGCAAGCATCATGGCTGGATAAAATTCAGCAAACTGTACAGAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTT
















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|211535329|gb|FL357693.1|FL357693
EST:     ATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
genomic: ATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
EST: gi|211178585|gb|FL326372.1|FL326372
EST:     ATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
genomic: ATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
EST: gi|211310066|gb|FL216070.1|FL216070
EST:     TGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
genomic: TGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
EST: gi|211310069|gb|FL216073.1|FL216073
EST:     TGACCATGATGAGCATGTTGAGTCCTATAGATCTGATGATGACCATAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACA
genomic: TGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACA
EST: gi|211310065|gb|FL216069.1|FL216069
EST:     TGACCATGATGAGCATGTTGAGTCCTATAGATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
genomic: TGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
EST: gi|211072830|gb|FL342711.1|FL342711
EST:     ATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
genomic: ATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
EST: gi|31359162|gb|CD443519.1|CD443519
EST:     TGACCATGATGAGCATGTTGAGTCCTATAGATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
genomic: TGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
EST: gi|67026048|gb|CO454797.1|CO454797
EST:     TGACCATGATGAGCATGTTGAGTCCTATAGATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
genomic: TGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTG
EST: gi|211421681|gb|FL309079.1|FL309079
EST:     ATCTGATGATGACCAGAAAG                         ATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGA
genomic: ATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGA
EST: gi|211310068|gb|FL216072.1|FL216072
EST:     TGACCATGATGAGCATGTTGAGTCCTATAGATCTGMTGATGACCAGAAAG                         ATTTVACTGAGCCAGGACATGCATCGTGG
genomic: TGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGG

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: 195

AAATATGAAGATGAAGAGTTTGATCATGAGTCAGAAGATGAATATGTTGATGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 240

AAATATGAAGATGAAGAGTTTGATCATGAGTCAGAAGATGAATATGTTGATGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 282

AAATATGAAGATGAAGAGTTTGATCATGAGTCAGAAGATGAATATGTTGATGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

AAATATGAAGATGAAGAGTTTGATCATGAGTCAGAAGATGAATATGTTGATGACCATGATGAGCATGTTGAGTCCTATAAATCTGATGATGACCAGAAAGgtgatcacca ... gctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcttgttctgtttatgtgattctgatttgttaatgtttatttgctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT
                              tgttaat  putative branch site (score: 325)
                                              ctattcc  putative PPT
                           atttgttaatgtttat  TA-rich tract