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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttctccaagtatatatggatcaagcatgatattttttatgtttgccaacttgaatttcacaaaataccatttttctatctgatagtatgaagctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG

Basic information

species Zea mays
transcript GRMZM2G129268_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 5
gtatgtttttctccaagtatatatggatcaagcatgat--atttt-ttatgtttgccaacttgaatttcacaaaataccatttttctatctgatagtatgaagctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG
||| | ||     | |  |||||||   ||| ||| ||  ||||| || | ||| | |   |   ||  || |||| |||| || ||||||||| ||  |||  ||  ||||| |||||||||| |||||| || ||||| |||||| ||||||| ||||||   ||||| ||||||||||||||||| ||||| ||||| || |||||||
gtacgcttcctgtccaa-atatatgacccaatcataatcaattttgttgttttttctactgttgtttcaactaaattccatgtt-ctatctgatggtgagaa-tttaacagGTGATGAGTGTAAAAGCTCTCGGCATTGCATTGAAGTTAACATTCTCAGGAGTGAACCAGTTATTCTATCCTCAGACATGGGCTTTTGCCCTAATTGTAG

upper sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtttttctccaagtatatatggatcaagcatgatattttttatgtttgccaacttgaatttcacaaaataccatttttct--atctgatagtatgaagcttt---gcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG
||||||  || |    ||||       || ||  ||  ||  ||||| | |    |   |||| |      || ||| ||| |   |  ||||| | | || |||     ||||| |||||||||| ||| |||||||| || || ||||| || || ||||||||||| || ||||| |||||||| || |||   ||  |  || | ||| 
gtatgtagttttt--ggtat------ttccagtttgtaatcctttatttctttaga--agaatgttg----attccactttgcctaaattgatattgtcaaacttgtgaacagGTAATGAGTGTAAAAGCACTTGGAATAGCATTAAAGCTGACCTTTTCAGGAACAAATCAGTTATTTTATCCTCAAACATGGATATTCACCTTGGTCGTAC
















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|211394432|gb|FL356656.1|FL356656
EST:     CAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACG                         GTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGA
genomic: CAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACGgtatgttttt ... agctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGA
EST: gi|60355925|gb|DN222898.1|DN222898
EST:     CAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACG                         GTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGA
genomic: CAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACGgtatgttttt ... agctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGA
EST: gi|60355918|gb|DN222891.1|DN222891
EST:     CAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACG                         GTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGA
genomic: CAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACGgtatgttttt ... agctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGA

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), 48 (downstream exon)
Score: 37

TGCAGCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACGgtatgttttt ... agctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

TGCAGCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACGgtatgttttt ... agctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

TGCAGCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACGgtatgttttt ... agctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

TGCAGCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTATGTTCTCTTCTGGGATCACTCACGgtatgttttt ... agctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttgaatttcacaaaataccatttttctatctgatagtatgaagctttgcagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTGTCAGGAACAAACCAATTATTCTATCCTCAGACTTGGGCCTTTGCACTGATTGTAG
                               atctgat  putative branch site (score: 66)
       aatttcacaaaata  TA-rich tract