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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT

Basic information

species Zea mays
transcript GRMZM2G092517_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092517_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g60960.1 (Oryza sativa), 3'ss of exon 2
gtaaagcctcaacttgaagaaaaaatcgtgcttt---tctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT
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gtacgatacca--ttacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatg-cggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAATCTGCGGCTGCGCGACCCCGTGTACGGCTGCATGGGCGCCATCT

upper sequence: GRMZM2G092517_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G40470.1 (Arabidopsis thaliana), 3'ss of exon 2
--gtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaa-acgtgtcgattgtca------cagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT
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ttattactctgtatttcactatgcaaaccctgttaaaagaaaaaaagattaatggttttggcaaaattctcacaatgtgtaacaattccaaactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
















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|101393630|gb|EB818747.1|EB818747
EST:     CCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTG                         GAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
genomic: CCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
EST: gi|101393628|gb|EB818746.1|EB818746
EST:     AGCAACGTCTCCAAGATGTTCTTG                         GAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
genomic: AGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
EST: gi|211271838|gb|FK962424.1|FK962424
EST:     CCGCCGTCCACAAGGTCTTCGGCGCTASSAACGTCTCCAAGATGCTCTTG                         GAGGTGGTGGAGGGGGAGA
genomic: CCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGA

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 3 RNA-Seq libraries.


Block sizes: 23 (upstream exon), 31 (downstream exon)
Score: 2

GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT


Block sizes: 31 (upstream exon), 29 (downstream exon)
Score: 5

GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT


Block sizes: 38 (upstream exon), 35 (downstream exon)
Score: 6

GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT
     tatagttaaaagattt  TA-rich tract