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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaagacgctttcatattttccttcattaattatgctcttacatgtattactaaaagccatctctttttcgtctgttctagaataattgaactcgatgcgtgtatgcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACCGATAAGTTCCTCAAACAGGCATTTGTTGCCGCGTCCATCAAGTTCCCAA

Basic information

species Zea mays
transcript GRMZM2G478212_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G478212_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g32830.2 (Oryza sativa), 3'ss of exon 1
gtgagaagacgctttcatattttccttcattaattatgctcttacatgtattactaaaagccatctctttttcgtctgttctagaataattgaactcgatgcgtgtat-gcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACCGATAAGTTCCTCAAACAGGCATTTGTTGCCGCGTCCATCAAGTTCCCAA
                   |  ||  ||| | |  |||| |  |      |  | |     |||  | |     || |  ||   ||   ||| ||   |  |  | |   || |  | ||| | ||||| ||||| ||||||||||| || ||||| ||| |||| |||||||| || ||||| || |  || ||||||||||||||||| |
--------------gtgagtcgtcaatcagtcaaaatgcacgcagcctcgtcgcgatttcgcatgacctgccgatc-gaactgacatgcgtgagctatgtatggattttatagCTCGTCGGGATCGCGCACCTGCTGGTGTCGCTGGGGATCGTGCTGGCCTCCGACAAGTTCCTGAAGCAGGCGTTCGCGGCGGCGTCCATCAAGTTCCCCA
















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|211082179|gb|FL396890.1|FL396890
EST:     CTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACC                         ATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACC
genomic: CTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACCgtgagaagac ... gtgtatgcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACC
EST: gi|211213409|gb|FL105881.1|FL105881
EST:     CTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACC                         ATTCTTGGGGT
genomic: CTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACCgtgagaagac ... gtgtatgcagATTCTTGGGGT
EST: gi|211213407|gb|FL105879.1|FL105879
EST:     CTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACC                         ATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACC
genomic: CTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACCgtgagaagac ... gtgtatgcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACC

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 14 (downstream exon)
Score: 7

TCAGCGATCTTCATCGCCCGACCTTCGTCGCAGCCTGATCGTCCTCAAGTCTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACCgtgagaagac ... gtgtatgcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACCGATAAGTTCCTCAAACAGGCATTTGTTGCCGCGTCCATCAAGTTCCCAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 28

TCAGCGATCTTCATCGCCCGACCTTCGTCGCAGCCTGATCGTCCTCAAGTCTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACCgtgagaagac ... gtgtatgcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACCGATAAGTTCCTCAAACAGGCATTTGTTGCCGCGTCCATCAAGTTCCCAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 45

TCAGCGATCTTCATCGCCCGACCTTCGTCGCAGCCTGATCGTCCTCAAGTCTACTGCTGGTACAGGAGGTGGCAATGCTTCCTCAGGACTGCTGCCCACCgtgagaagac ... gtgtatgcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACCGATAAGTTCCTCAAACAGGCATTTGTTGCCGCGTCCATCAAGTTCCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagccatctctttttcgtctgttctagaataattgaactcgatgcgtgtatgcagATTCTTGGGGTGGCGCATCTGCTTGTGTCGCTGGGCATTGTGCTCGCCACCGATAAGTTCCTCAAACAGGCATTTGTTGCCGCGTCCATCAAGTTCCCAA
                        tagaataatt  TA-rich tract