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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttatttggagacctgatatctatatttgattatttatcacgaagcatgaatatgccttttcttatactgtctaccaccatgaatattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATCAGGTAACTACTGACCAGCAACACCCCAGCACCACCATTTTGCAGCATTT

Basic information

species Zea mays
transcript GRMZM2G052699_T02
intron # 7
splice site 3'
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|67023575|gb|CO452324.1|CO452324
EST:     GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
EST: gi|31356932|gb|CD441289.1|CD441289
EST:     GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
EST: gi|71432148|gb|DR813198.1|DR813198
EST:     GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
EST: gi|60359717|gb|DN226690.1|DN226690
EST:     AAAAGAAAGAAGCAAAGGAGGGAAAGCGTCGTTCACGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: AAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
EST: gi|32937986|gb|CF042805.1|CF042805
EST:     GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
EST: gi|71435075|gb|DR816125.1|DR816125
EST:     GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
EST: gi|91872362|gb|EB402319.1|EB402319
EST:     AAAGAAAGAAGCAATGGAGGGAAAGGGTCGTTCTCGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: AAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
EST: gi|32935392|gb|CF040204.1|CF040204
EST:     GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         ATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC
genomic: GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATC

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), 49 (downstream exon)
Score: 34

TCATCACAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATCAGGTAACTACTGACCAGCAACACCCCAGCACCACCATTTTGCAGCATTT


Block sizes: 37 (upstream exon), 42 (downstream exon)
Score: 7

TCATCACAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATCAGGTAACTACTGACCAGCAACACCCCAGCACCACCATTTTGCAGCATTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 15

TCATCACAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATCAGGTAACTACTGACCAGCAACACCCCAGCACCACCATTTTGCAGCATTT


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 27

TCATCACAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcttatttg ... tattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATCAGGTAACTACTGACCAGCAACACCCCAGCACCACCATTTTGCAGCATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgaagcatgaatatgccttttcttatactgtctaccaccatgaatattctgcagATTCATCAAGAAACAGTGGGTAAGTGAATAGTTGACATGTGTAGAGTGATCAGGTAACTACTGACCAGCAACACCCCAGCACCACCATTTTGCAGCATTT
                  ttttcttata  TA-rich tract