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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcttcatacagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC

Basic information

species Zea mays
transcript GRMZM2G047219_T01
intron # 6
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 6
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 6
gtagcttcatacagtggaagacacgtaactgtagatccatgcttttctcaaactcttgtga-aagtgctaactctatagtttgattgatctgtgg------ctttcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC
              |  | |   |   | | |         | |  |    | | || |   ||||||| | ||| | |  | ||  |||||||       ||||||| ||||||| |||||||| || ||| ||| |||||||||||||||||||||||||||||| |||||||||||    || || || || || ||||| |||||| | |
--------------taaaggttgcaacattctctgcttgcacatgccatgtatttttatatcaagtgctgattctgttgcctaatccatctgtgcctgttcctttcctttgcagGCCTTGCTATTTGAGGAGGCAAGGTTTAAGGCATTTGATCTGGCATCAAAACCTGAAGGTGAAGGAGTACCTACAACTGATTTCAGGGCTCTTTTTTCGC
















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|17931616|gb|BM268576.1|BM268576
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|94473462|gb|EB702420.1|EB702420
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|148966373|gb|EE017367.2|EE017367
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATCCAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|13381992|gb|BG458667.1|BG458667
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|211140552|gb|FL174090.1|FL174090
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|16380015|gb|BI993261.1|BI993261
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|148955762|gb|EC901460.2|EC901460
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|32940932|gb|CF045751.1|CF045751
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|211028260|gb|FL437885.1|FL437885
EST:     CAGAAMCAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|89762676|gb|DY690164.1|DY690164
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTTATCTGGCATCAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAA
EST: gi|5706289|gb|AI942065.1|AI942065
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|74243387|gb|DT651301.1|DT651301
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|16919596|gb|BM074268.1|BM074268
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|6742502|gb|AW313317.1|AW313317
EST:     CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAA
EST: gi|91055640|gb|EB166058.1|EB166058
EST:     CAGAAACA-GAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAG                         GCATTGCTATTCGAAGAGTCAAAAGTT-AAGGCATTTGATCTGCCATCAAA
genomic: CAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAA-GTTTAAGGCATTTGATCTGGCATCAAA

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), 48 (downstream exon)
Score: 64

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 25

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TGGTGGCTTGCGAGAGTTGATTGTTGGGAAGGATGATGAGATCCTGAAAACAGAAACAAGAACTATAGCCAGGGCCGATGTTGCAGAAGTTTGCATACAGgtagcttcat ... tcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgtgaaagtgctaactctatagtttgattgatctgtggctttcctatgcagGCATTGCTATTCGAAGAGTCAAAGTTTAAGGCATTTGATCTGGCATCAAAACCAGAAGGTGAAGGGACGCCAACTACAGACTTTAGGGCACTTTTTGCAC
                                          ctttcctat  CT-rich tract
                     tatagttt  TA-rich tract