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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaactttctgtttctataaactgccctagttctttttcatacagcttacgaaatccacagtgcgttaggggcaatcaacattgtattcttacatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAGTCATCTTGAGGCGACCACCTAGCGGTGTGACGAGCTAACTCTTGTTGCA

Basic information

species Zea mays
transcript GRMZM2G015610_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015610_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g37660.1 (Oryza sativa), 3'ss of exon 8
gtataaactttctgtttctataaact-gccctagttctttttcatacagcttacgaaatccacagtgcgttaggggcaatcaacattgtattcttacatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAGTCATCTTGAGGCGACCACCTAGCGGTGTGACGAGCTAACTCTTGTTGCA--
|| || | | ||||| ||| || | ||| | | | | || | || | || | || | |||||| ||||| |||||||| || |||||||||||||||| | || ||||||||||||| | | || ||| | | | |||| | | ||
-----------------gtacaactttgttacagttccattttatgcgacttgtcagtccaaagtcacatttg-------taatagagtcctgttgtacatgcagATTCCTCCTCAAGAAACAGTGGGTCAAGTGAATAGTAGCCAAGTT--GGAGTCATCTTGAAGAAATCATCTAACAGCTTTCTGAGCGATAACGCATTAGTTG
















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|60395327|gb|DN228196.1|DN228196
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|211383182|gb|FL436925.1|FL436925
EST:     GAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: GAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|71436497|gb|DR817547.1|DR817547
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|60344692|gb|DN211665.1|DN211665
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|60341906|gb|DN208879.1|DN208879
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|60357724|gb|DN224697.1|DN224697
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|149074571|gb|EE162972.2|EE162972
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|89759152|gb|DY688060.1|DY688060
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|71430015|gb|DR811065.1|DR811065
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|78026416|gb|DV494803.1|DV494803
EST:     AGTTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: AG-TTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|60349214|gb|DN216187.1|DN216187
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|67021753|gb|CO450502.1|CO450502
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|88746951|gb|DY531092.1|DY531092
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGGGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
EST: gi|60338391|gb|DN205364.1|DN205364
EST:     CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAG                         ACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG
genomic: CAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAG

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: 159

TCGTCAAAGACAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAGTCATCTTGAGGCGACCACCTAGCGGTGTGACGAGCTAACTCTTGTTGCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 57

TCGTCAAAGACAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAGTCATCTTGAGGCGACCACCTAGCGGTGTGACGAGCTAACTCTTGTTGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

TCGTCAAAGACAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAGTCATCTTGAGGCGACCACCTAGCGGTGTGACGAGCTAACTCTTGTTGCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 63

TCGTCAAAGACAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGTTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGTCACTCGCGAGgtataaactt ... acatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAGTCATCTTGAGGCGACCACCTAGCGGTGTGACGAGCTAACTCTTGTTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacgaaatccacagtgcgttaggggcaatcaacattgtattcttacatgtgcagACTCCTCGTCAAGAAATAGCGGGTCAAGTGAATAGTGACTAAAGCCAGGAGTCATCTTGAGGCGACCACCTAGCGGTGTGACGAGCTAACTCTTGTTGCA
                                        ttcttac  putative branch site (score: 63)
 ttcttac  CT-rich tract
 attgtatt  TA-rich tract