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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgttctaaaaatggcatttttaatcttttctttcttattagtatccccttcatatcatttgttattaatctaaatgtgttgtttttttggcatag

Basic information

species Zea mays
transcript GRMZM5G886952_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G886952_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 4
GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgttctaaaaatggcattt--ttaatcttttctttcttattagtatccccttcatatcatttgttattaatctaaatgtgttgtttttttggcatag
|||||||||||| ||||  ||||||||||||||||| || |||||||||| |||||||||||||||| |  |||||||||||  | | |  |   |||  |||| || ||  || | |  | | |    ||  |||  | ||| ||||                            
GATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCTgtaagtgtgtgttgatagcgttctttgcttaacctctttcttttcagca-tctgaaattactattttatgtcattag---------------------------
















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|60356786|gb|DN223759.1|DN223759
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
EST: gi|211487045|gb|FL021472.1|FL021472
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCANGGGGAACAGTTTGTATGGNTCACTCCCTCCTGAACTGGGGG
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCA-GGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGA
EST: gi|149109166|gb|EE190051.2|EE190051
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
EST: gi|148951631|gb|EC897373.2|EC897373
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGAGAACAGTTTGTATGGGTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
EST: gi|31360094|gb|CD444451.1|CD444451
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGGGAACAGTTTGGATGGGTCACTCCCTCCTGAACTGGGG
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGG
EST: gi|149087972|gb|EE177200.2|EE177200
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCCTC-TGAACTGGGGA
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCC-TCCTGAACTGGGGA
EST: gi|149087580|gb|EE176978.2|EE176978
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
EST: gi|31354140|gb|CD438497.1|CD438497
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
EST: gi|31349376|gb|CD433733.1|CD433733
EST:     GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT                         GTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA

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: 183

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGCTGCAACAATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGCTGCAACAATT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 24

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGCTGCAACAATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTTgtaagtgtgt ... tttggcatagGTCACTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGCTGCAACAATT