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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcattttggactgagttatgtttttgtctgggtagtggcatgttttgcatgtcttggttggttgtttttttctgcgaggaaaataaagccttgta...

Basic information

species Zea mays
transcript GRMZM2G147450_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147450_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 3
CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcattttg--gactgagttatgtttttgtctgggtagtggcatgttttgcatgtcttggttggttgtttttttctgcgaggaaaataa--agccttgta--------------------------------------------------------------------
|||| || || || || ||||||||||| |||| ||||||||||||||| || |||||||||||||| |||||||| || || || |||||  ||||||||||| |||  |    |  ||||| |||   ||   ||  |  ||   || ||   ||||  |  |||     || || |||  ||  ||| ||  | |||  |                                                                     
CTCGGCTCGTTCTTGAGGATGGTTCAGTTTGGAAGGCCAAGTCTTTTGGTGCTTCAGGAACACAAGTTGGTGAAGTGGTATTTAATACATCTTTGACAGGgtaaatcaactaaccgtttgagtgatggcatt---tgtttcctgttgtggttgagatgtgcttattg-----ttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcag

upper sequence: GRMZM2G147450_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G39390.1 (Glycine max), 5'ss of exon 2
CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcattt-tggactgagttatgtttttgtctgggtagtggcatgttttgcatgtct--tggttggttgtttttttctgc-gaggaaaataaagccttgta--
|| | ||||| || |||||||||||| | ||||| || || || ||||| || ||||| || ||||| || || ||||||||||| |||||| ||||||||| ||  |  | || |    |  |||| | | |||   |  |||| |   |||||||     |   ||| || |||| | ||  | |     |      || |   
CTAGACTTGTGCTTGAAGATGGTTCAATTTGGAGAGCAAAATCGTTTGGTGCTTCAGGGACCCAAGTTGGCGAGGTTGTTTTCAATACATCATTGACAGGgtgaggaaactatgaatcttgggatgtgtgtttctttttcatggctttgcttgcatgctgaatatgtggctggttttctttgttgtgttgtgtgtgtgattatcag

upper sequence: GRMZM2G147450_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G15510.3 (Glycine max), 5'ss of exon 2
CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagt-cattttggact----gagttatgtttttgtctgggtagtggc-atgttttgcatgtcttggttggttgtttttttctgcgaggaaaataaagccttgta
|| | ||||| || |||||||||||| | ||||  || || || ||||| || || || || ||||| || |||||||||||||| |||||| ||||||||| ||   | | || |      ||    |||| || | | |||  ||      |  |  |||  | |||||||| || |||  || |  |    |       |   
CTAGACTTGTGCTTGAAGATGGTTCAATTTGGAAAGCAAAATCGTTTGGTGCTTCGGGGACTCAAGTTGGCGAAGTTGTTTTCAATACATCATTGACAGGgtgaggatactatgaatcttgggatgcgtgttctttttttggttttgcttgcatgctaaatgagt-ggttggtt-ttctttgttgtgttgtgtgtgtgattctcag

upper sequence: GRMZM2G147450_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ19894 (Selaginella moellendorffii), 5'ss of exon 2
CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcattttggactgagttatgtttttgtctgggtagtggcatgttttgcatgtcttggttggttgtttttttctgcgaggaaaataaagccttgta
|  | ||||| ||  | ||||| ||||||||||  | |||||||||||| || || ||||| |||||||| |||||||||||||| ||  |  |||| ||||| ||  || |      | ||  | |     |     | |   | || ||||||||| |     |                                  
CAAGGCTTGTTCTTCAGGATGGATCAGTGTGGAATGGCAAGTCTTTTGGAGCTTCTGGAACGCAAGTCGGAGAAGTTGTTTTCAATACTGCCATGACCGGgtatgtatttctctttccattttggatcacaac----cactttaaagtgttgcatgtccttcccag----------------------------------

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|148969716|gb|EE020588.2|EE020588
EST:     GCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGG                         CTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGAT
genomic: GCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcatt ... gtggttgcagCTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGAT




















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: 160

CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcatt ... gtggttgcagCTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGATGACCAATCCCCATATTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcatt ... gtggttgcagCTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGATGACCAATCCCCATATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcatt ... gtggttgcagCTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGATGACCAATCCCCATATTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 72

CTCGTCTTGTCCTGGAAGATGGTTCAGTGTGGAGGGCCAAGTCTTTTGGCGCATCAGGAACACAAGTCGGTGAAGTTGTTTTCAACACATCACTGACAGGgtaagtcatt ... gtggttgcagCTATCAGGAGATTTTGACAGATCCAAGCTATGCTGGTCAATTTGTCCTGATGACCAATCCCCATATTG