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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttacccctcgtcttgcatatacgttgttacacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttctcagctctttttcgttgcatttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG

Basic information

species Zea mays
transcript GRMZM2G047219_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047219_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 3
gtaaatgttacccctcgtcttgcatatacgttgtt---acacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttc-tcagctctttttcgttgcatttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG
|||||   |   | | |||||||| ||   || ||   ||   |        | ||||  | |    ||| |   |  | ||   || | ||    ||  ||     |   | || |  ||||||      |  | | |   | ||  || ||| |      ||||||||  ||| || ||| ||| |||||||| |||| ||| ||  | |||||||| ||||||||||| || |||||  |||||||||| ||||| ||||||||||||||||||||||||
gtaaaacat---ctttgtcttgcagatggattctttgaacttgtttcttttcagctatgctgttctttaaaccagt--attatcaatgacttgttggt--ctagctagcatagctcctttttttttcagttaattcattccttgttcatgattcgtttatgttttttcgt--catcttcatgtagCCAAGAGCATTGGTGTAAAACAGGTGGTTTTGGTTGGATCCATGGGCGGCACAGATGTCAATCACCCACTAAATAAGTTAGGAAATGCAAATATACTG
















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|50331999|gb|CO527125.1|CO527125
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211142589|gb|FL359509.1|FL359509
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGAGGA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGGAGGA
EST: gi|211529297|gb|FL356731.1|FL356731
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGAGGA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGGAGGA
EST: gi|17931616|gb|BM268576.1|BM268576
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|149015400|gb|EE045246.2|EE045246
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211267296|gb|FL319984.1|FL319984
EST:     -TGGATTGGATTGGCCAAAAGAATCAA-TTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGAGGA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGGAGGA
EST: gi|148966373|gb|EE017367.2|EE017367
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|12045929|gb|BF728159.1|BF728159
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211072521|gb|FL326767.1|FL326767
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|148996959|gb|EE035773.2|EE035773
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|74243388|gb|DT651302.1|DT651302
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCNAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|89251955|gb|DY623741.1|DY623741
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|76293497|gb|DV033065.1|DV033065
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|78180658|gb|DV550986.1|DV550986
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCAC
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCAC
EST: gi|32848760|gb|CD988441.1|CD988441
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|148955762|gb|EC901460.2|EC901460
EST:     AAGAATCAAATTGATGGGG                         TTAAGAGCATCGGGGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: AAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|211394348|gb|FL351051.1|FL351051
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTTGGTGGGATCCATGGGGAGT
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTT-GGTGGGATCCATGGG-AGG
EST: gi|148966374|gb|EE017368.2|EE017368
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGG
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGG
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|16919596|gb|BM074268.1|BM074268
EST:     ATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: ATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|6742502|gb|AW313317.1|AW313317
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|71774203|gb|DR972081.1|DR972081
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG                         CTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA
genomic: GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAA

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: 86

GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 483

GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 35

GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 318

GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgtta ... ttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacgtaactttctatttctgtttctcagctctttttcgttgcatttttatgcagCTAAGAGCATCGGTGCAAAGCACATAGTTTTGGTGGGATCCATGGGAGGAACAGACATCAATCACCCGCTAAACAAGTTAGGAAATGCAAATATACTG
  acgtaac  putative branch site (score: 318)
                                          cattttt  putative PPT
                                           atttttat  TA-rich tract