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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggcttattttctcttaacaattttttttggccttgccgtgagccctacattttccgattcaatcaacctagctgacttagctcattgtgttgtag

Basic information

species Zea mays
transcript GRMZM2G050961_T06
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050961_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g41710.1 (Oryza sativa), 5'ss of exon 5
GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggcttattttctct-taacaatt---ttttttggccttgcc-----gtgagccctacattttccgattcaatcaacctagc---tgacttagctcattgtgttgtag------------------------------------------------------------------------------------
||||||||||| ||||| |||||||||||||||| ||  ||   |||||  ||||   |   |||| ||| ||| |      ||   |||| | |      |   |  ||||||||     ||  |  | | |  |  | ||                                                                                     
GTTCTCTTCTCTGACATAAATGCTTATGAGgtaaatgaattggcttctccctaacggatacattttgtggtctttctcctaagtactccctccgtcccaaaaaaaaggcaacctagaaggggatgtgacccctcctagtataacgaatctgaaaggagggagtacgatgccttttttggtttttgttccagtcatctgaacgctcatggtattgcatgtacttgcag

upper sequence: GRMZM2G050961_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv15s0021g00830.t01 (Vitis vinifera), 5'ss of exon 6
GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggcttattttctcttaacaattttttttggccttgccgtgagccctacattttccgattcaatcaacctagctgacttagctcattgtgttgtag
||||| ||||||||||| |||||||||||||||| |  || | | | |   ||  |  ||| ||    | ||  | |     |  |  |    ||     ||  || ||     |    |   |  | |  
GTTCTTTTCTCAGACATAAATGCTTATGAGgtaaata-ctgactctgtagaaattaagtttattcatatagcacttaatatgatttactagcctttttcaaaggtacctttacaaatggaagttcctatcc
















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|113796158|gb|DW913371.1|DW913371
EST:     AGACATCAATGCTTATGAG                         GTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
genomic: AGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
EST: gi|166466537|gb|EG225135.1|EG225135
EST:     GTTCTCTTCTCAGACATCAATGCTTATGAG                         GTGGAGCTTGG
genomic: GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGG
EST: gi|211349701|gb|FL449949.1|FL449949
EST:     GTTCTCTTCTCAGACATCAATGCTTATGAG                         GTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
genomic: GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
EST: gi|6342692|gb|AW165516.1|AW165516
EST:     GTTCTCTTCTCAG-CATCAATGCTTATGAG                         GTGGAGCTTGGTACTGATGACGAGAAGCACTGCTTCTGCCGTGAGTCAGNC
genomic: GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
EST: gi|113799136|gb|DW919645.1|DW919645
EST:     CTCAGACATCAATGCTTATGAG                         GTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
genomic: CTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
EST: gi|13249748|gb|BG360653.1|BG360653
EST:     GTTCTCTTCTCAGACATCAATGCTTATGAG                         GTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
genomic: GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
EST: gi|6431818|gb|AW172022.1|AW172022
EST:     GTTCTCTTCTCAGACATCAATGCTTATGAG                         GTGGAGCTTGG-ACTGATGACGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
genomic: GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
EST: gi|211485848|gb|FK973440.1|FK973440
EST:     GTTCTCTTCTCAGACATCAATGCTTATGAG                         GTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC
genomic: GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGAC

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), 40 (downstream exon)
Score: 159

GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGACTTGTTAGCTGTAGTTGAATGAATTTTACCATGAAAATTTCGGACTTACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 370

GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGACTTGTTAGCTGTAGTTGAATGAATTTTACCATGAAAATTTCGGACTTACC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 108

GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGACTTGTTAGCTGTAGTTGAATGAATTTTACCATGAAAATTTCGGACTTACC


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 197

GTTCTCTTCTCAGACATCAATGCTTATGAGgtaactggct ... tgtgttgtagGTGGAGCTTGGTACTGATGAAGAGAAGCACTGCTTCTGCCGTGAGTCAGACTTGTTAGCTGTAGTTGAATGAATTTTACCATGAAAATTTCGGACTTACC