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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatattctttcatttttattgcgatttacatttgtgtgaaggatctccacaaatatttatgtagaaggagtgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG

Basic information

species Zea mays
transcript GRMZM2G130034_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130034_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 7
gttagcatattctttcatt-tttat---tgcgatttacatttgtgtgaaggatctccac-aaatatttatgtag---aaggagtgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG
|||||||| | | |||||| || ||   || | ||||||||  | |||| | || |||| | |||||||  | |   ||| |   || ||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| ||  |||||||||||||||||||||| ||||| || ||||
gttagcatttccattcattcttcatccatgtggtttacattattttgaaaggtccccaccacatatttacatgggtaaagaaactttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG

upper sequence: GRMZM2G130034_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------gttagcatattctttcatttttattgcgatttacatttgtgtgaaggatctcc-acaaatatttatgtagaaggagtgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG
                       ||      | | ||  | |||  ||    ||||   |  ||   | |||||   ||   ||| | | |    ||||       |||||||||||| ||| ||||||| || || |||||| |||| || |||||||||||  | ||||| ||||| |||||||| ||||| || || |
tagctgtcaaaatttgaagccttgtggaagcaattttataatttagttat--tttattgtgctgaacaagatcttttactgttatatgtatgattggag-------cagAAATGATGCAGGATTGGCAGCTGCAGAGTTAGCACTAGCTGTTGAGAAACATGTGTTAGAATCTGGATCTATTGATACTGTTGGTACTGTGG
















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|148941174|gb|EC886056.2|EC886056
EST:     ACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCCTGCA-G                         AAATGATGCTGGACTG
genomic: ACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCC-TGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTG
EST: gi|33466598|gb|CF243647.1|CF243647
EST:     AGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAG                         AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
genomic: AGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
EST: gi|78022951|gb|DV491338.1|DV491338
EST:     GACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAG                         AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
genomic: GACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
EST: gi|71775246|gb|DR973124.1|DR973124
EST:     GTCATGCTGGAGCAGTGCTGATGCCTGCAAG                         AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
genomic: GTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
EST: gi|31359313|gb|CD443670.1|CD443670
EST:     GACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAG                         AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
genomic: GACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
EST: gi|91874397|gb|EB404354.1|EB404354
EST:     GGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAG                         AAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
genomic: GGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACA
EST: gi|148940595|gb|EC885401.2|EC885401
EST:     ACTTTGAAGGGAAATGGCG-TCATGCTGGAGCAGTGCTGATGCCTGCAAG                         AAATGATGCTGGACTG
genomic: ACTTTGAAGGGAA-TGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTG

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: 53

TCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 37

TCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 31

TCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 35

TCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGCAAGgttagcatat ... tgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatttgtgtgaaggatctccacaaatatttatgtagaaggagtgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG
                         aaatatttatgtagaa  TA-rich tract