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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgctgcacatttatcagtagcaacacaattttgtatcatgtagatgtttattgatctgaaatgtgatctatgtgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATCCTTGCGAGGCCAATGATGTACCTTGCGCTGACTTACGACC

Basic information

species Zea mays
transcript GRMZM2G079538_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 12
gtaactgctgcacatttatcagtagcaacacaattttgtatcatgtagatgtttattgatctga---aatgtgatctatgtgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATCCTTGCGAGGCCAATGATGTACCTTGCGCTGACTTACGACC
||  ||  | ||  |||  || | |||| |         |  | || ||| || ||| ||||||   ||||| || ||| |  | |||||||  ||||||| || ||||| |||||||| |||||||||||||| ||| | ||  |||| || ||||||||||||||||||||||||||||| || ||||
gtc-ctttttcatttttgccacttgcaaaaattgccctcactaggttgatattcattcatctgacacaatgt-atatatatctaatgcagTCTGCTATTCTTGGAATGCACTCCATTGTACAACGCCCTGTGGTCGTGGACGGCAACATTCTCGCGAGGCCAATGATGTACCTTGCGCTGACATATGACC
















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|211104575|gb|FL031921.1|FL031921
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGKGCAACGCCCTGTGGTTGKGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6102024|gb|AW126494.1|AW126494
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|110528815|gb|EE032999.1|EE032999
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTTTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|31363969|gb|CD448324.1|CD448324
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6021309|gb|AW066237.1|AW066237
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|13558099|gb|BG549455.1|BG549455
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|13558422|gb|BG549778.1|BG549778
EST:     GTGGTGTCTATGGAAGCTTTTTCTGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|31358903|gb|CD443260.1|CD443260
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|4804479|gb|AI665349.2|AI665349
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|211169880|gb|FL077609.1|FL077609
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCNTNCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAA
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAA
EST: gi|32830086|gb|CD969764.1|CD969764
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|211174261|gb|FL479898.1|FL479898
EST:     CTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: CTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|211081302|gb|FL464951.1|FL464951
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|13558100|gb|BG549456.1|BG549456
EST:     GCGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTG
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTG
EST: gi|6654256|gb|AW267661.1|AW267661
EST:     CTCCTCAGCACACCTATCATCAACCCTCCNCAG                         TCGTTTTTTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: CTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32942914|gb|CF047733.1|CF047733
EST:     GTGGTGTCTATGGAAGCCTCCTCAACACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32933424|gb|CF038236.1|CF038236
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|60358853|gb|DN225826.1|DN225826
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6227238|gb|AW155837.1|AW155837
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTG-GGTTG
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTG
EST: gi|166470787|gb|EG142344.1|EG142344
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGG
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGG
EST: gi|149009739|gb|EE154080.2|EE154080
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTTTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|211169873|gb|FL077602.1|FL077602
EST:     TGGTGTCTATGGAAGCCTCCTCAGCACACCTAATCATCAACCCTC-ACAG                         TCGTCTATTCTGGGGATGCATT
genomic: TGGTGTCTATGGAAGCCTCCTCAGCACACCTA-TCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATT
EST: gi|148978724|gb|EE026282.2|EE026282
EST:     GTGGTGTTTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTTTATTTTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32867029|gb|CF006711.1|CF006711
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|8368148|gb|BE051093.1|BE051093
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|78022452|gb|DV490839.1|DV490839
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|14548407|gb|BI096736.1|BI096736
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|166524759|gb|EG130537.1|EG130537
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCA
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCA
EST: gi|32858121|gb|CD997802.1|CD997802
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|13562254|gb|BG550474.1|BG550474
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|24766295|gb|CA401450.1|CA401450
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|21626137|gb|BQ621058.1|BQ621058
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32867030|gb|CF006712.1|CF006712
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|67019048|gb|CO447797.1|CO447797
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|44900266|gb|CK826811.1|CK826811
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAG                         TCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT

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: 47 (upstream exon), 49 (downstream exon)
Score: 123

GGCGCTCTCAATTGATGACATGGCAGGTGGAACATTCACCATCTCCAACGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATCCTTGCGAGGCCAATGATGTACCTTGCGCTGACTTACGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

GGCGCTCTCAATTGATGACATGGCAGGTGGAACATTCACCATCTCCAACGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATCCTTGCGAGGCCAATGATGTACCTTGCGCTGACTTACGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 214

GGCGCTCTCAATTGATGACATGGCAGGTGGAACATTCACCATCTCCAACGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATCCTTGCGAGGCCAATGATGTACCTTGCGCTGACTTACGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 150

GGCGCTCTCAATTGATGACATGGCAGGTGGAACATTCACCATCTCCAACGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCTCCACAGgtaactgctg ... tgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATCCTTGCGAGGCCAATGATGTACCTTGCGCTGACTTACGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgtatcatgtagatgtttattgatctgaaatgtgatctatgtgaattgcagTCGTCTATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAATGGTGACATCCTTGCGAGGCCAATGATGTACCTTGCGCTGACTTACGACC
                     tattgat  putative branch site (score: 150)
                atgtttatt  TA-rich tract