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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGCTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttctgccttgtttttgttaaagatatatatatgcgtgctttatttagttaggttggtggaattccgtgttttggagcgttttcagacgttgtta...

Basic information

species Zea mays
transcript GRMZM2G038313_T01
intron # 1
splice site 5'
intron type U2

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|30704721|gb|CD058585.1|CD058585
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|86467968|gb|DY234338.1|DY234338
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|76919397|gb|DV167695.1|DV167695
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCT
EST: gi|148933758|gb|EC877689.2|EC877689
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|148943093|gb|EC888147.2|EC888147
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|71333152|gb|DR803610.1|DR803610
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|211179411|gb|FL363899.1|FL363899
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|67042197|gb|CO468452.1|CO468452
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|149075427|gb|EE163945.2|EE163945
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|71438188|gb|DR819238.1|DR819238
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|211277761|gb|FL330399.1|FL330399
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|211180554|gb|FL306734.1|FL306734
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|149070764|gb|EE159177.2|EE159177
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|148996096|gb|EE035357.2|EE035357
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|71429761|gb|DR810811.1|DR810811
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|149077453|gb|EE166147.2|EE166147
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
EST: gi|211193900|gb|FL366188.1|FL366188
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCA
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCA
EST: gi|71318808|gb|DR796165.1|DR796165
EST:     TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAG                         ATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT
genomic: TCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTT

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: 396

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGCTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCCTGGGCTGCTGAGTACCTGTACCAGTATCGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 270

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGCTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCCTGGGCTGCTGAGTACCTGTACCAGTATCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGCTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCCTGGGCTGCTGAGTACCTGTACCAGTATCGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 354

CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGCTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttct ... aacaatgcagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCCTGGGCTGCTGAGTACCTGTACCAGTATCGTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAGCCCCGCTCGTCGCCTTCCTCCAGAACCCGCAGCTCGTGCAGGAGCTCAGGCCCGACAAACAGTACAACATCCACATGCTCCAGGAGAGATACCAGgtctgcttctgccttgtttttgttaaagatatatatatgcgtgctttatttagttaggttggtggaattccgtgttttggagcgttttcagacgttgtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA