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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgcacattaacaatttgttggcagttttttgtttgtggttattagtcgatgcataattataatgtacatggtggtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTG

Basic information

species Zea mays
transcript GRMZM2G027756_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027756_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os07g32400.1 (Oryza sativa), 3'ss of exon 15
gtgatgcacattaacaatttgttggcag-ttttttgtttgtggttattagtcgatgcataattataatgtacatggtggtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTG
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gtgatgcacatgaatg--ttgttggcaaatttctcaattgtggttaatggttgatacttattcata-tatttg-ggtaattaatgcagGCAAAGGCTGCTCTCCAGGCTGCGTTTAAAAAGGGTAATGCTCGTGAAAGACATGTTATCAGCAAACATGAAAAGGAATCACATGAACCCAGAATTTCGG
















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|60350165|gb|DN217138.1|DN217138
EST:     AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAG                         GCAAAGGCTGCTTTGCAGGCTGGGT-AAGAAAGGGAAA
genomic: AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAA
EST: gi|71773326|gb|DR971232.1|DR971232
EST:     AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAG                         GCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
genomic: AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
EST: gi|32931563|gb|CF036375.1|CF036375
EST:     AAAAAGCATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAG                         GCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
genomic: AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
EST: gi|76282536|gb|DV022104.1|DV022104
EST:     AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAG                         GCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
genomic: AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
EST: gi|32930056|gb|CF034868.1|CF034868
EST:     AAAAAGCATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAG                         GCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
genomic: AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
EST: gi|33091466|gb|CF051460.1|CF051460
EST:     AAAAAGCATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAG                         GCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA
genomic: AAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGA

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: 38 (upstream exon), 48 (downstream exon)
Score: 123

TGAAGACCCAGAAACTCCACGATCTTCAAGGTCAAGGCTGGGGATCCAAGAAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 33

TGAAGACCCAGAAACTCCACGATCTTCAAGGTCAAGGCTGGGGATCCAAGAAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 23

TGAAGACCCAGAAACTCCACGATCTTCAAGGTCAAGGCTGGGGATCCAAGAAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 78

TGAAGACCCAGAAACTCCACGATCTTCAAGGTCAAGGCTGGGGATCCAAGAAAAAACATCAAATGCTCCTCTTGAGGATAGTGCCATTAACCTTGCAGAGgtgatgcaca ... gtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttgtggttattagtcgatgcataattataatgtacatggtggtacatgcagGCAAAGGCTGCTTTGCAGGCTGGGTTAAGAAAGGGAAATGCTCGAGAAAGACCTTTTATCAACAGGCATGAAAAGGGATCACATGAGCATAGATCTTCTG
                        ataattataatgtaca  TA-rich tract