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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacattagcaacttgagaactcacagtgtgtattgatactagaactgaacgcaatttgtgcagaccggcagactggttttactctccgtttggcttgcagGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGGATCAGTGGCATCCTTTCATGGGGCCACTGCGGTTCATCCAAGTTCTGTTCCTCT

Basic information

species Zea mays
transcript GRMZM2G477340_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G477340_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g48060.1 (Oryza sativa), 3'ss of exon 10
aacattagcaacttgagaactcacagtgtgtattgatactaga-actgaacgcaatttgtgcagaccggcag---actggttttactctccgtttggcttgcagGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGGATCAGTGGCATCCTTTCATGGGGCCACTGCGGTTCATCCAAGTTCTGTTCCTCT
 | ||   ||  ||| | | | ||| | ||  || | |||  | |||  |   |  |||  |  |    |||   || |   || || | | ||     |||||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||| | ||||||||||||||  |||||||| | |||||  ||||||| |
-atatgcaca-tttgtgcagttacattctgc-ttcagactgcatactatagttaggttgaacccatttacagtttaccgaccttcctttac-ttgcatatgcagGTGAAAAGATCACTGAGCCAGTTCACCCCTGCACAATGGGACAAGGATCAATGGTACCCTTTCATGGGGCCGTTGCGGTTCGTTCAAGTGTTGTTCCTGT
















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|33099446|gb|CF059406.1|CF059406
EST:     TGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGG                         GTAAGGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGG
genomic: TGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGGgtaaggtatg ... tggcttgcagGT--G---AAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGG
EST: gi|33099553|gb|CF059513.1|CF059513
EST:     TGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGG                         GTAAGGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGG
genomic: TGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGGgtaaggtatg ... tggcttgcagGT--G---AAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGG
EST: gi|33100318|gb|CF060278.1|CF060278
EST:     TGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGG                         GTAAGGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGG
genomic: TGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGGgtaaggtatg ... tggcttgcagGT--G---AAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGG

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: 35 (upstream exon), 21 (downstream exon)
Score: 2

GTATTTGGGCAGGAATGCACACAGTCCGTTACTTTGATGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGGgtaaggtatg ... tggcttgcagGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGGATCAGTGGCATCCTTTCATGGGGCCACTGCGGTTCATCCAAGTTCTGTTCCTCT


Block sizes: 48 (upstream exon), 30 (downstream exon)
Score: 6

GTATTTGGGCAGGAATGCACACAGTCCGTTACTTTGATGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGGgtaaggtatg ... tggcttgcagGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGGATCAGTGGCATCCTTTCATGGGGCCACTGCGGTTCATCCAAGTTCTGTTCCTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 17

GTATTTGGGCAGGAATGCACACAGTCCGTTACTTTGATGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGGgtaaggtatg ... tggcttgcagGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGGATCAGTGGCATCCTTTCATGGGGCCACTGCGGTTCATCCAAGTTCTGTTCCTCT


Block sizes: 47 (upstream exon), 17 (downstream exon)
Score: 2

GTATTTGGGCAGGAATGCACACAGTCCGTTACTTTGATGGCAAAACATATGAATGGGTCGGACTGAGCCGCCAACGAAGCATCATGGgtaaggtatg ... tggcttgcagGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGGATCAGTGGCATCCTTTCATGGGGCCACTGCGGTTCATCCAAGTTCTGTTCCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacgcaatttgtgcagaccggcagactggttttactctccgtttggcttgcagGTGAAAAGATCGCTGAGCCAGTTCACCCCTGCTCAATGGGACAAGGATCAGTGGCATCCTTTCATGGGGCCACTGCGGTTCATCCAAGTTCTGTTCCTCT
                               ttttactctccgttt  CT-rich tract
       aatttgt  TA-rich tract