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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtgttactgtgcccttggtcttaagtgtccacaaccttacagtggaatgaaatagatcggtagatctgctgaaattaatctgaaagaatttaagatcgtatggatatgcgaattgagaatcacaaaagttccattactgaaacactataccgaacgcaccaatttattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG

Basic information

species Zea mays
transcript GRMZM2G045259_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 14
gtatatgtgttactgtgcccttggtcttaagtgtccacaaccttacagtggaatgaaatagatcggtagatctgctgaaattaatctgaaagaatttaagatcgtatggatatgcgaattgagaatcacaaaagttccattactgaaacactataccgaacgcaccaatttattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG
|| | | | | || || || | ||| | |||| | | | || | | | ||| | | || | | ||| | ||| | | | | || | ||||||||||||| || ||||||||||||||||| ||||| || ||||| || ||||| | ||| |||||||| || ||||| || |||||||| ||||||| ||
-----------------------------------------------gtacgtttggagtgtccaagagccttgtaaaattgaattc-----attttagcagca---agctacactgactatcaattgaatatgtaaaagtcttgagattttatt---atctcgcatatctcttttgtagGTAGTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATAGTGGTTATCGCATAACTGCAACAGCAGCCACATGTGACCAGGTGG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 14
gtatatgtgttactgtgcccttggtcttaagtgtccacaaccttacagtggaatgaaatagatcggtagatctgctgaaattaatctgaaagaatttaagatcgtatggatatgcgaattgagaatcacaaaagttccattactgaaacactataccgaacgcaccaatttattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG----
|| | | | | || || || | ||| | |||| | | | || | | | ||| | | || | | ||| | ||| | | | | || | ||||||||||||| || ||||||||||||||||| ||||| || ||||| || ||||| | ||| |||||||| || ||||| || |||||||| ||||||| ||
-----------------------------------------------gtacgtttggagtgtccaagagccttgtaaaattgaattc-----attttagcagca---agctacactgactatcaattgaatatgtaaaagtcttgagattttatt---atctcgcatatctcttttgtaggtagTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATAGTGGTTATCGCATAACTGCAACAGCAGCCACATGTGACCAGGTGGCTTT
















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|8516441|gb|BE123167.1|BE123167
EST:     GAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAG                         GTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGG
genomic: GAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgt ... tattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGG
EST: gi|67025278|gb|CO454027.1|CO454027
EST:     GAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAG                         GTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGG
genomic: GAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgt ... tattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGG
EST: gi|9956162|gb|BE643596.1|BE643596
EST:     GAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGCTTCACTTCTCAG                         GTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGG
genomic: GAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgt ... tattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGG

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: 49 (upstream exon), 49 (downstream exon)
Score: 226

AAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGCAACAGCTGGAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgt ... tattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

AAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGCAACAGCTGGAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgt ... tattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

AAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGCAACAGCTGGAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgt ... tattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 239

AAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGCAACAGCTGGAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgt ... tattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaaaagttccattactgaaacactataccgaacgcaccaatttattttgtagGTAGTGGAGCTTGATTTCTTATATCCAAGTGAGGGCATCCACATGCGTTGGGACAATGGCTATCGCATTACGGCAACGGCTGCCACATGGGACCAGGCGG
                                           tttatttt  CT-rich tract
 aatttattttgta  TA-rich tract