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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccagctgatacctgggcatgctattttttctgcagttttattttttcaatatcactaacaaacaaatcaatttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG

Basic information

species Zea mays
transcript GRMZM2G012284_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 10
gtaaccagctgatacctgggcatgctattttttctgcagttttattttttcaatatcactaacaaacaaatcaatttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG
|||     |  || ||  |||||    |||| | || ||| |   |||||    |||| | | ||      || ||| ||||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||||||||||
gtatttgacatatcccatggcatttccttttctatgtagtatc--ttttttggaatcattgataacg----cattttttttcagATGGGGAGGAACTTTGATGAACTCGTTCCTGTTTAATGTTGGACTCATCCTACTTTGCTCCATCAG

upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 10
---------gtaaccagctgatacctgggcatgctattttttctg--cagtt-ttattttttcaatatcactaacaaacaa-atcaatttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG
          ||||| | |   || |      ||||||||    |  || |  |||  || ||   ||  || |    | | ||||| || ||||||||||||||  ||| |||||||||| ||||| || ||||| || ||||| || ||||| || |||||
gtaatccatctaaccggtttcaacattatttggctattttccaaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG

upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaac-cagctgata-cctgggcatgctatttttt-ctgcag------ttttattttttcaatatcactaacaaaca-aatcaatttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG
||||  || ||  ||   | |  ||| | |||  |  | |||      || | |||| |     |  || | || |  ||| || ||||||||||||||||| |||| | |||||||| || || |||||||| || ||||| || || || || |||||
gtaattcatcttgtagttttgaaatgttttttgctatttcagagatctttctgttttcttctggtttctcataagcctaattaacttgtttcagATGGGGAGCCACTCTTATGAACTCTTTTCTCTTTAATGTCGGTCTCATTCTCCTCTGTTCTATCAG

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|76288405|gb|DV027973.1|DV027973
EST:     ATTGAAGTTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: ATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|67039856|gb|CO466111.1|CO466111
EST:     GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|76288406|gb|DV027974.1|DV027974
EST:     GAGATGATGCTTGGATTGAAGTTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|38568991|gb|CF974876.1|CF974876
EST:     GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|91872772|gb|EB402729.1|EB402729
EST:     GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|67024981|gb|CO453730.1|CO453730
EST:     GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|71763789|gb|DR961726.1|DR961726
EST:     GAGATGATGCTTGAATTGAAGCTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|71449543|gb|DR830593.1|DR830593
EST:     GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
EST: gi|33942467|gb|CF349067.1|CF349067
EST:     GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAA                         ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT
genomic: GAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACT

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: 48 (upstream exon), 49 (downstream exon)
Score: 380

CTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 409

CTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 466

CTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 615

CTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCACAATTCACCCGATGAAgtaaccagct ... tttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgcagttttattttttcaatatcactaacaaacaaatcaatttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG
                           cactaac  putative branch site (score: 615)
                                             tttgtttc  putative PPT
          ttttattttttcaata  TA-rich tract