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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggtgttaatggaagcatttctcttgatatattcattcatcagcaaatatggaatgaaactttctgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGCCGTCATTCTGGGCCTGGAAAGGTGGTGAAAGCAGGCTCTCTAAGTTGCA

Basic information

species Zea mays
transcript GRMZM2G176699_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176699_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g54900.1 (Oryza sativa), 3'ss of exon 3
gtaagggtgttaatggaagcatttctcttgata-------tattcattcatcagcaaatatggaatgaaactttctgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGCCGTCATTCTGGGCCTGGAAAGGTGGTGAAAGCAGGCTCTCTAAGTTGCA---
|||||  | |||    |||||||| |    |||       || |   || | ||||||||||  |  | ||||||||||||||||| |||  ||||||    |  |   ||||||| ||| |||| |||||| | || ||||||||||||||||||| ||||||||| |||||  | ||||||||   
gtaagtctattagcataagcattttttacaataccattcctaatttctcgtgagcaaatatgata-aacactttctgttgtctagGTAGATACAATCAAGTTGCCC---GTCCTCTACATGTCCACTATGTTGCACCATCATTCTGGGCCTGGAAAGATGGTGAAAGAAGGCTTGCAAAGTTGCATAA
















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|33468054|gb|CF245103.1|CF245103
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|89251960|gb|DY623746.1|DY623746
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|148934449|gb|EC878487.2|EC878487
EST:     TACAATTGATTCCAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCATAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|78090762|gb|DV519136.1|DV519136
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|148934293|gb|EC878319.2|EC878319
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|71771081|gb|DR969018.1|DR969018
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|71439989|gb|DR821039.1|DR821039
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|31350639|gb|CD434996.1|CD434996
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|74244436|gb|DT652350.1|DT652350
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|71764590|gb|DR962527.1|DR962527
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|50334194|gb|CO529320.1|CO529320
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
EST: gi|93282885|gb|EB675149.1|EB675149
EST:     TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAAT                         GCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC
genomic: TACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 48

ATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCTGTGGTTACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGCCGTCATTCTGGGCCTGGAAAGGTGGTGAAAGCAGGCTCTCTAAGTTGCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 14

ATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCTGTGGTTACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGCCGTCATTCTGGGCCTGGAAAGGTGGTGAAAGCAGGCTCTCTAAGTTGCA


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 3

ATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCTGTGGTTACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGCCGTCATTCTGGGCCTGGAAAGGTGGTGAAAGCAGGCTCTCTAAGTTGCA


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 33

ATTGAGGATAGTGCAAATGCGGCTATGCTATTTCAACCTCATGCTGTGGTTACAATTGATTCAAAGGGTTTTTCTTTTCGACTGTTGAAGCAACTGAAATgtaagggtgt ... tgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGCCGTCATTCTGGGCCTGGAAAGGTGGTGAAAGCAGGCTCTCTAAGTTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttgatatattcattcatcagcaaatatggaatgaaactttctgttgtctagGCAGAAGCAATCAGAAGGTTCAAAGTCCTCTGCATATCCATTATGTTTCGCCGTCATTCTGGGCCTGGAAAGGTGGTGAAAGCAGGCTCTCTAAGTTGCA
  tcttgat  putative branch site (score: 33)
                                        ctttctgtt  putative PPT
       atatattcattcat  TA-rich tract