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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatctaaggataatgatatgaattgaatcctcatgcctctgtatttttataacttcaacaacatgttcgtatatttctgtgattggatttattcttatatcgctttctgcattttggtag

Basic information

species Zea mays
transcript GRMZM2G177970_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177970_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g54020.1 (Oryza sativa), 5'ss of exon 11
ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggat-ctaaggataatgatatgaattgaatcctcatgc-ctctgtatttttataacttcaacaacatgttcgtatatttctgtgattggatttattcttatatcgctttctgcattttggtag
||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||   | ||| ||       ||||||    ||| |||   |  |||  | ||   | | |  || ||   |  || ||  |  | | | |  |  |   |  |   |||              
ATGTCGAAGTCTGCTCCTTCAGATCAGTCTCGTATTAACCTTCTTGATCCAAAAGATgtaagggcaccaagaat-------tgaatt---ccctgatgtgtttcgtaaatatagtgcataactaatat---caaattttattacgctagcacatggtagaaggtgcattt--------------

upper sequence: GRMZM2G177970_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT2G25840.2 (Arabidopsis thaliana), 5'ss of exon 9
ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatctaaggataatgatatgaattgaatcctcatgcctctgtatttttataacttcaacaacatgttcgtatatttctgtgattggatttattcttatatcgctttctgcattttggtag
|||||||||||||| ||||| || ||||| || ||||| || |||||| |||||||||||||    |||    |||||  | | |    | ||  ||  | |||  || |    || | | | |   |||  ||   ||  |  | | |  ||                             
ATGTCCAAGTCTGCCCCTTCTGATCAGTCCCGGATTAATCTCCTTGACTCAAAAGATgtaag----taa----aatgaactcactcatgttctt-tgtatgtgttcttgttctgctactaaatccatttctcatccctcctt--tcgaaaatag----------------------------

upper sequence: GRMZM2G177970_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 5'ss of exon 11
ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatctaaggataatgatatgaattgaatcctcatgcctctgtatttt--tataacttcaacaacatgttcgtatatttctgtgattggatttattcttatatcgctttctgcattttggtag
||||||||||||||| ||||||| ||||||||||| ||||||||||||||||||||||| ||            |||| ||   |||  |   | || | || | ||||  ||| | ||    ||| | | |   |   |   |  ||  | ||  ||  ||                      
ATGTCCAAGTCTGCTTCTTCAGATCAGTCTCGTATCAACCTTCTTGACCCAAAAGATgtgagt---------cgatgacatttcttgtctttgc-tgtcactattttttggtatcatttttttaacct-tccacttgggtagatagtttaagtttatccaatgcaaaa----------------

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|32944158|gb|CF048977.1|CF048977
EST:     AGTCTGCTCCTTCAGACCAATCTCGTATTAACCTTCTTGACCCAAAAGAT                         GTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
genomic: AGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
EST: gi|32930432|gb|CF035244.1|CF035244
EST:     AGTCTGCTCCTTCAGACCAATCTCGTATTAACCTTCTTGACCCAAAGGAT                         GTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
genomic: AGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
EST: gi|71449703|gb|DR830753.1|DR830753
EST:     AGCCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT                         GTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
genomic: AGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
EST: gi|32930572|gb|CF035384.1|CF035384
EST:     AGTCTGCTCCTTCAGACCAATCTCGTATTAACCTTCTTGACCCAAAGGAT                         GTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
genomic: AGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
EST: gi|78120427|gb|DV538811.1|DV538811
EST:     AGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT                         GTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG
genomic: AGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG

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), 46 (downstream exon)
Score: 46

ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 81

ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 26

ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 30

ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGATgtaaggatct ... attttggtagGTGATTGCAAATAAGATCAAGCGCTGCAAAACTGACTCATTCCCAGG