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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaattcatggcattgcatagtgtattagattgcctttgcaaatcttctatgaacatgcttacctgaagattatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG

Basic information

species Zea mays
transcript GRMZM2G058702_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058702_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 3'ss of exon 3
gtatggaattcatggcattgcatagtgtattagattgcctttgcaaatcttctatgaac-atgcttacctgaagatt-----atttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG
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gtatggaacc--tgatgtttca--gtcttgtagatcgttgttgaaaaacatgtgaaaattgtacttacctgaagaattggtggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG
















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|67018197|gb|CO446946.1|CO446946
EST:     AGTGAAGAAAGCACGAGTAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|78114407|gb|DV532796.1|DV532796
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACCCTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|67011881|gb|CO440630.1|CO440630
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|149044909|gb|EE047713.2|EE047713
EST:     CAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: CAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|91054581|gb|EB164999.1|EB164999
EST:     CAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: CAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|60357361|gb|DN224334.1|DN224334
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|78027609|gb|DV495996.1|DV495996
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|78122472|gb|DV540856.1|DV540856
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|149111402|gb|EE294905.2|EE294905
EST:     CAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: CAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|211437264|gb|FL422462.1|FL422462
EST:     AAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|91054582|gb|EB165000.1|EB165000
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|211115866|gb|FL470201.1|FL470201
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|32939307|gb|CF044126.1|CF044126
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|148943508|gb|EC888569.2|EC888569
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|31349054|gb|CD433411.1|CD433411
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACTTTTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|4827706|gb|AI668398.1|AI668398
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|71432412|gb|DR813462.1|DR813462
EST:     AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|12970194|gb|BG266861.1|BG266861
EST:     AAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTGCACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|6827927|gb|AW331570.1|AW331570
EST:     AGTGAAGAAAGCCCGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTG                         GGACTTTTACCCTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATG

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: 44 (upstream exon), 49 (downstream exon)
Score: 70

CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 91

CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 19

CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 109

CTGGATATATATTTGCTCTCGCAAAATTGGAAGGATCTAGTGAAGAAAGCACGAGCAAAACAGCTCCAACCAAATGAGTACAGCTCTGgtatggaatt ... ttatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagattgcctttgcaaatcttctatgaacatgcttacctgaagattatttgcagGGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG
                               tgcttac  putative branch site (score: 109)
                                         aagattattt  TA-rich tract