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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcattagaccagcatgatgttacattgttacacacccactgggtgggtgttaggttccttgcactgatttattgtgctttcgtgcag

Basic information

species Zea mays
transcript GRMZM2G158021_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 5'ss of exon 9
CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcat---tagaccagcatgatgttacattgttacacacc--cactgggtgggtgttaggttccttgcactgatttattgtgctttcgtgcag
 ||  |||| |||||||| || ||||| ||||||||||||||||||||||||||| ||||   |  || |  |  ||||| |  ||  |    |   |  |   | || | ||   ||||   | | ||||     ||||| ||||||
TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattcttcaactactaccatgtttcgctgccatgatctatctttttttaggggatat-ctcctaatattaatttgggaggcttt-gtgcag

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA06G15180.2 (Glycine max), 5'ss of exon 9
CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcattagaccagcatgatgttacattgttacacacccactgggtgggtgttaggttccttgcactgatttattgtgctttcgtgcag--------------------------------------------
 ||| |||| |||||||| |||| |||||| |||||||| ||||||||||||||    | |  ||     | |  |||  || |    || || ||   |  || ||   || ||   |||  |||||| | ||  |  | ||                                            
TGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAGgttgatactgtacttaatttacattattttttgcttcatcctct--tttcgtattgtatttct---act--tttattcttctccctcgtagttgaacatgtcacctactaagtggaatatgttgttgcgtaccag

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA04G39690.1 (Glycine max), 5'ss of exon 9
CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcattagaccagcatgatgttacattgttacacacccactgggtgggtgttaggttccttgcactgatttattgtgctttcgtgcag---------------------------------------
 ||| |||| |||||||| ||||  ||||| |||||||| ||||||||||||||    |||  ||     | |  |||  ||      || || ||   |  |||||  ||| ||     |  | |  |      | ||  ||                                       
TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattgtacttaatttactttatttttggcttcatcctct--ttttgtgttgtgtttctacttttattcttctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccag

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|78025510|gb|DV493897.1|DV493897
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|60398886|gb|DN231702.1|DN231702
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|29544633|gb|CB605013.1|CB605013
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|6827378|gb|AW331021.1|AW331021
EST:     CTCTGGTATGGGGTTGCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|32934872|gb|CF039684.1|CF039684
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|29543482|gb|CB605568.1|CB605568
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|60358587|gb|DN225560.1|DN225560
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|4886224|gb|AI677344.1|AI677344
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|74240037|gb|DT647951.1|DT647951
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|14203739|gb|BG837416.1|BG837416
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|211345618|gb|FL479628.1|FL479628
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|211493768|gb|FL172984.1|FL172984
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|32932341|gb|CF037153.1|CF037153
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|71758265|gb|DR956202.1|DR956202
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|86472109|gb|DY238479.1|DY238479
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|32933065|gb|CF037877.1|CF037877
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|211493769|gb|FL172985.1|FL172985
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|30088250|gb|CB886455.1|CB886455
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|22542064|gb|BU092502.1|BU092502
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGAC
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGAC
EST: gi|71418754|gb|DR804530.1|DR804530
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|29544505|gb|CB604885.1|CB604885
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|5108308|gb|AI740021.1|AI740021
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATTAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
EST: gi|32916029|gb|CF020841.1|CF020841
EST:     CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAG                         GAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG
genomic: CTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAG

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), 49 (downstream exon)
Score: 295

CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAGGCGTATCATGTGGTGGAACGAAACCTGTTTTTTTCTGCAAAACTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAGGCGTATCATGTGGTGGAACGAAACCTGTTTTTTTCTGCAAAACTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAGGCGTATCATGTGGTGGAACGAAACCTGTTTTTTTCTGCAAAACTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcatta ... tttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAGGCGTATCATGTGGTGGAACGAAACCTGTTTTTTTCTGCAAAACTGGGAG