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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTGGAAGTATGGAGTCTGCCTTAGAACTGCTAGCATCAACTCCATATTGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttattaccttttggaacaacatattgtacatgtattctgttgctgcatgtcatgtgttgcaatgctattcacccttctggaatatttttgtgtag

Basic information

species Zea mays
transcript GRMZM2G005990_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005990_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 5'ss of exon 2
TCTGTGGAAGTATGGAGTCTGCCTTAGAACTGCTAGCATCAACTCCATATTGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttattaccttttggaacaacatattgtacatgtattctgttgctgc-atgtcatgtgttgcaatgctattcaccct--tctggaatatttttgtgtag
|||||||||| ||| | ||||| || ||||| ||| ||||||||||||| || ||||| ||||||||||| ||||||||||| || || || ||||| ||||||| | ||| ||||||  | | ||| | |||  |  ||| ||||| | |  | |  |      |||  ||||||||| |  |||| || ||||   |||||
TCTGTGGAAGCATGAACTCTGCATTGGAACTACTATCATCAACTCCATACTGTTTATCCATTGAGAAAGTTTTTGTTATAGGGGGTGGACAAGTACTAAGgtgagctgttaacttttgccaaagcatctagtatgtaaattgtgttgtttctgtatactccacctcaactctattcacctttatctgtaaaatttcactgtag

upper sequence: GRMZM2G005990_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 1
TCTGTGGAAGTATGGAGTCTGCCTTAGAACTGCTAGCATCAACTCCATATTGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttattaccttttggaacaacatattgtacatgtattctgttgctgcatgtcatgtgttgcaatgctattcacccttctggaatatttttgtgtag--
| |||||||| |||  |||||| || |||||| ||||  |  |||| || |   | |||||||||||||| |||||||||||||| || ||| || | ||||     ||     |||  || |   | || | |||    ||  |     | | ||||||   ||  |  | ||     |    ||  |||||  ||||   
TATGTGGAAGCATGTCGTCTGCATTGGAACTGTTAGCTGCTTCTCCTTACTCTCTGTCAATTGAGAAAGTATTTGTTATAGGAGGTGGTCAGATATTTAGgta---catctttctttaaaatattttgttcttcatccgctccttc----cttttcatgttaagctct-ttctttgttatagctgataattttcatgtacag
















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|211156125|gb|FL360792.1|FL360792
EST:     TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAG                         AGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
genomic: TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
EST: gi|50331960|gb|CO527086.1|CO527086
EST:     TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAG                         AGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
genomic: TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
EST: gi|33466387|gb|CF243436.1|CF243436
EST:     TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAG                         AGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
genomic: TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
EST: gi|149014441|gb|EE044050.2|EE044050
EST:     TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAG                         AGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
genomic: TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
EST: gi|91873333|gb|EB403290.1|EB403290
EST:     TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAG                         AGAATATCTTACAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA
genomic: TGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCA

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), 47 (downstream exon)
Score: 142

TCTGTGGAAGTATGGAGTCTGCCTTAGAACTGCTAGCATCAACTCCATATTGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCAGTCGAGCATTGAGTGTGACACTTTCATCCCTCCGGTTGACTTCTCAGTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 74

TCTGTGGAAGTATGGAGTCTGCCTTAGAACTGCTAGCATCAACTCCATATTGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCAGTCGAGCATTGAGTGTGACACTTTCATCCCTCCGGTTGACTTCTCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

TCTGTGGAAGTATGGAGTCTGCCTTAGAACTGCTAGCATCAACTCCATATTGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCAGTCGAGCATTGAGTGTGACACTTTCATCCCTCCGGTTGACTTCTCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

TCTGTGGAAGTATGGAGTCTGCCTTAGAACTGCTAGCATCAACTCCATATTGCTTATCAATTGAGAAAGTGTTTGTTATAGGAGGCGGGCAGGTACTGAGgtgagttatt ... ttttgtgtagAGAATATCTTAAAGGACCTGCATGTGAGGCTATCCATCTAACTGACATTCAGTCGAGCATTGAGTGTGACACTTTCATCCCTCCGGTTGACTTCTCAGTG