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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccatttagaccgtactgagcagtgtatactgcaatttttatagagtgggatttgaaatatgataggccgctggaaatatgatgaattcgttctcta...

Basic information

species Zea mays
transcript GRMZM2G043893_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043893_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g24650.1 (Oryza sativa), 5'ss of exon 7
GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccatttagaccgtactgagcagtgtatactgcaatttttatagagtgggatttgaaatatgataggccgctggaaatatg-atgaattcgttctcta-----
|| || ||||| ||||| || || ||||||||||| ||||| |||||||| ||||| ||||| |  ||||||||||||||||  | |||      |   ||  |    |  | | |||  ||| || ||  || ||  |  |   |      || |||| || ||       | || |      
GTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAGgtaatgagttaattttga--aagttgctcgtgtt-ctattgatat-gactgccatctgtgaagttccatatt--tgaaaatttgtataggacattgctattgttgg

upper sequence: GRMZM2G043893_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G36530.1 (Glycine max), 5'ss of exon 7
GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccatttagaccgtactgagcagtgtatactgcaatttttatagagtg-----ggatttgaaatatgataggccgctggaaatatgatgaattcgttctcta
||  | ||||| ||||| || || || ||||| ||||| || ||| |||| ||||||||||||||||||||||| ||||||    | || || |   ||     | | |  | | ||   | ||   |        ||    || |   |||||| |     |    |   ||| | |     
GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAGgtataactgtatacagctatgcatt-tatttctttctatacctgtaatatccccataaatcatcaaaactctaggcctccc---acccaaaagatttgcttagc-

upper sequence: GRMZM2G043893_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA17G08150.1 (Glycine max), 5'ss of exon 7
GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccatttagaccgtactgagcagtgtatactgc----aatttttatagagtgggatttgaaatatgataggcc-gctggaaatatgatgaattcgttctcta
||  | ||||| ||||| || || || ||||| ||||| || ||| |||| ||||||||||| ||||||||||| ||||||     |||  | |   ||     | |  |        |||  | | ||     | | |        | ||    |||    || | |  | ||  ||     
GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAGgtataacattacgcagccatgcattctttccatccttataaatcataaaagctccaggtctccctcccaaaagatttgcttagcatttaa-aattttattt----

upper sequence: GRMZM2G043893_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA16G19350.1 (Glycine max), 5'ss of exon 7
GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccatttagaccgtactgagcagtgtatactgc----aatttttatagagtgggatttgaaatatgataggcc-gctggaaatatgatgaattcgttctcta
||  | ||||| ||||| || || || ||||| ||||| || ||| |||| ||||||||||| ||||||||||| ||||||     |||  | |   ||     | |  |        |||  | | ||     | | |        | ||    |||    || | |  | ||  ||     
GTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAGgtataacattacgcagctatgcattctttccatccttataaatcataaaagctccaggtctccctcccaaaagatttgcttagcatttaa-aattttattt----

upper sequence: GRMZM2G043893_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA19G22730.1 (Glycine max), 5'ss of exon 7
GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgta-accatttagaccgta---ctgagcagtgtatactgcaatttttatagagtgggatttgaaatatgataggccgctggaaatatgatgaattcgttctcta
||  ||||||| ||||| ||||| |||||||| ||||| || ||| |||| |||||||||||||| |||| ||| ||||||  |   |  ||   |    ||    | | | |||   |||  | || | | ||  | |    | | |     | ||   | |    |  | |    | |||
GTTAATAACACAGATGCAGAGGGTAGGCTTACCCTGGCAGATGCTCTGGTGTATGCTTGTAACCAGGGTGCTGAAAAGgtatgctgctatgaatctgaatctttctaatatttacataaatcataattgtgaggtgtatactctttaagttaactctaccagt----tagagttaaccccta

upper sequence: GRMZM2G043893_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 5'ss of exon 7
GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccatttagaccgtactgagcagtgtatactgcaatttttatagagtgggatttgaaatatgataggc----cgctggaaatatgatgaattcgttctcta
||  ||||||| ||||| ||||| || || ||||| || ||||||||||| |||||||||||||||||||| || |||||| |||  |  |  |  || |    |   |   |   ||||| |      | | ||||| | || |  |     |  ||   |  | |  | |    ||| | 
GTCAATAACACAGATGCAGAGGGCAGACTCACACTTGCAGACGCTTTGGTATATGCTTGTAACCAAGGTGTAGAGAAGgta-ccaccttaaaagagctaa--tattcctgtagatttttttttctcagagaaattgaattttgtttcgtttttcattgatcaactaagtactagactcttt-

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|149080361|gb|EE169379.2|EE169379
EST:     TTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAG                         ATTATTGATCTGGCGACGTTAACGGGTGCTATTCGTGTCGCGCTTGGGCCC
genomic: TTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccattt ... tggtatgcagATTATTGATCTGGCGACGTTAACGGGTGCTATTCGTGTCGCGCTTGGGCCC




















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), 47 (downstream exon)
Score: 3

GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccattt ... tggtatgcagATTATTGATCTGGCGACGTTAACGGGTGCTATTCGTGTCGCGCTTGGGCCCAGCATCGCTG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 116

GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccattt ... tggtatgcagATTATTGATCTGGCGACGTTAACGGGTGCTATTCGTGTCGCGCTTGGGCCCAGCATCGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 213

GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccattt ... tggtatgcagATTATTGATCTGGCGACGTTAACGGGTGCTATTCGTGTCGCGCTTGGGCCCAGCATCGCTG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 19

GTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAGgtaaccattt ... tggtatgcagATTATTGATCTGGCGACGTTAACGGGTGCTATTCGTGTCGCGCTTGGGCCCAGCATCGCTG