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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacggatcgatccctccgcgtttcgacgagcgagcctggtggttttaatttggttagggttttgtttgtgctgacggagaggcggcgcatgcatttttacctgtgcag

Basic information

species Zea mays
transcript GRMZM2G416965_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g42090.1 (Oryza sativa), 5'ss of exon 1
---------------------------------------------------------------GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacggatcgatccctccgcgtttcgacgagcgagcctggtggttttaatttgg----ttagggttttgtttgtgctgacggagaggcggcgcatgcatttttacctgtgcag------
                                                               |||||||||||||||| ||||||||||||||||| ||||||  |  | ||  |    ||| ||| |  | |||  |  |  |   ||| ||  ||    || | |   |||  |  |||| | |    |    | ||   || |   ||||         
CTGCCATCTAGCTAGCAAAGATGATCTCCCCGGACGCGGCTCGCAACGTCGTCGGCATCATCGGCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCCGTgtaacta-agctctctaaacccg-gttgctgctagct-gtttaattaatttgatgagggtttttggtgagatgtgagaactgaagaattaacaaatcttgatcttgtttgtgtgtgtgtgcag

upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g08490.1 (Oryza sativa), 5'ss of exon 1
------------------------------------------GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagc--acggatcgatccctccgcgtttcgacgagcgagcctggtggttttaatttggttagggttttgtttgtgctgacggagaggcggcgcatgcatttttacctgtgcag
                                          ||||||||||||||||||||||||||||||| || |||    |   | |   ||||     |  |   |||| ||| | ||       | ||   ||    |    |      ||||    |  |   || |  |                 
ATGGTGTCCCggacttgatccgcaacgtggtgggcatcgtcggcaatgtcatctcctttggcctcttcctctcgccggtgcccaccttctggcggatcatcaagaataaggacgtgcgggact-------tcaaggcggaccagtacctagccacgctgctcaattgcatgctctag-----------------

upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g42110.1 (Oryza sativa), 5'ss of exon 1
-------------------------------------------GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacggatcgatccctccgcgtttcgacgagcgagcctggt---ggttttaatttggttagggttttgtttgtgctgacggagagg-cggcgcatgcatttttacctgtgcag
                                           |||||||||||||||| |||||||||||| |||| ||||||  | |      |      ||   ||||    | | |    |     |      | || ||   |        | ||||     |   | |    ||  | | ||  | |||||
ATGATCTCCCCGGACGCGGCTCGCAACGTCGTCGGCATCATCGGCAATGTCATCTCCTTCGGCCTCTTCCTCGCCCCCGTgtaattaagttcttctaatcaagccgatcgatcgaccatctctctctgcatgcaggataggatacaatacaacaaattctgaaattcatttctggttgtgtgtatatatgtatgcag

upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g08030.1 (Oryza sativa), 5'ss of exon 1
-----------------------------GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagc--acggatcgatccctccgcgtttcgacgagcgagcct----ggtggtttta-atttggttagggttt-----tgtttgtgctgacggagaggcggcgcatgcatt-tttacctgtgcag-----------------------------------------------------------------------------------
                             |||| |||||||||||||||||||||||||| || ||     |   | |    |||     |  |    |||     | ||    |   |      |  |||  |   |       ||| ||  |||         |||      |||  |  |||    |||                                                                                   
CATGATCCGCAACGTGGTGGGCATCGTCGGCAACGTCATCTCCTTTGGCCTCTTCCTCTCGCCGGTCCCCACCTTCTGGCAAATCATCAAGAATAAGAACgtataggacttcaagacagacccgtacctggccacactgctcaactgtatgctctgggacttttacggtctccccatcgtccaccccaacagcatcctcgtcgtcaccatcaacggcattggccttgtcatcgagacctgtctatctcaccatcttcttcctcttctccgacaag

upper sequence: GRMZM2G416965_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g07860.1 (Oryza sativa), 5'ss of exon 1
------GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgt--aagcacggatcgatccctccgcgtttcgacgagcgagcct----ggtggtttta-atttggttagggtt-----ttgtttgtgctgacggagaggcggcgcatgcatttttacctgtgcag----
      |||| |||||||||||||||||||||||||| || |||   |    | |   ||||     |  |    | | ||    ||    || ||      |  |||  | | |      |||  | ||||   ||     |  ||    |  | |   |  | |      
TCGTCGGCAACGTCATCTCCTTTGGCCTCTTCCTCTCGCCGGTGCCCATTTTCTGGCGGATCATCAAGAATAAGAATGTGCAGAACTTCAAGGCGGACCCgtacctggccacgctactcaattgcatatgctt-tgggtcttctacgtcctccctatcgtccatcccaacag

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|211351800|gb|FK980889.1|FK980889
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT                         GCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCC
EST: gi|211351797|gb|FK980886.1|FK980886
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT                         GCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCC
EST: gi|149079042|gb|EE167926.2|EE167926
EST:     GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGT                         TCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCC
genomic: GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCC
EST: gi|211351796|gb|FK980885.1|FK980885
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT                         GCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCC
EST: gi|211351798|gb|FK980887.1|FK980887
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCAGT                         GCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCC
genomic: GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCC

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: 10 (upstream exon), 41 (downstream exon)
Score: 7

GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCCTGACCCCTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAC


Block sizes: 9 (upstream exon), 41 (downstream exon)
Score: 1

GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCCTGACCCCTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAC


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 877

GCAATGTCATCTCCTTTGGCCTCTTCCTCTCCCCAGTgtaagcacgg ... acctgtgcagTCTGACGTTCTGGCGGATCTGCAAGGCCAGGGACGTGGAGGAGTTTAAGCCTGACCCCTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAC