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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcggtggcgctttgtccttcacggccggtcgtgttgcgtgtgggctgtcgtgctgatgagccttttttttttctcccccgcccgactcccgtgctgttcgtacgtgttgccag

Basic information

species Zea mays
transcript GRMZM2G063909_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g33240.1 (Oryza sativa), 5'ss of exon 2
TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcggtggcgctttgtc----cttcacggccggtcgtgt-tgcgtgtgggctgtcgtgctgatgagccttttttttttctcccccgcccgactcccgtgctgttcgtacgtgttgccag
                                |    |   |  |||| |||||||||||||||||||| |||||||| |||||  | |||||||||||||||||||| ||||   | |  ||     | || | |   |  | | ||| | || | ||| | |||||    || |||  |  | |  |  ||| |                             
-----------------------------GTCCACCCCTGCAGGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtttgctcgtgttgct-gccag-----------------------------

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 2
TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcggtggcgctttgtcc----ttcacggccggtcgtgt-tgcgtgtgggctgtcgtgctgatgagccttttttttttctcccccgcccgactcccgtgctgttcgtacgtgttgccag
                                            |||| |||||||||||||||||||| |||||||| |||||  | |||||||||||||||||||| ||||   | |  ||     | || | |   |  | | ||| | || | ||| | |||||    || |||  |  | |  |  ||| |                             
-------------------------------------------GCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATGgtgagtagtggtgatccatcatcgatcgtccatgtcaatttttttgtgcatttgtggtgtggcgctgaaattccgtttgctcgtgttgct-gccag-----------------------------

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 2
TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcggtggcgctttgtccttcacggccggtcgtgttgcgtgtgggctgtcgtgc--tgatgagccttttttttttctcccccgcccgactcccgtgctgttcgtacgtgttgccag
                    |||  | |  |  |   |||  ||||||||||||||||||| ||||||| |||||||| ||||| || ||||||||| |||||||         |   ||| | | |        | | | ||||| ||   |   ||||  |||  |    ||  ||  | |     | | |                             
-------------------CAGCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc-caacatcttg-catgcctattttctggcgatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcag-----------------------------

upper sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g10070.2 (Oryza sativa), 5'ss of exon 2
TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcggtggcgctttgtccttcacggccggtcgtgttgcgtgtgggctgtcgtgc--tgatgagccttttttttttctcccccgcccgactcccgtgctgttcgtacgtgttgccag
                      |  | |  |  |   |||  ||||||||||||||||||| ||||||| |||||||| ||||| || ||||||||| |||||||         |   ||| | | |        | | | ||||| ||   |   ||||  |||  |    ||  ||  | |     | | |                             
----------------------CTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc-caacatcttg-catgcctattttctggcgatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcag-----------------------------

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|71303469|gb|DR787844.1|DR787844
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|78076904|gb|DV505338.1|DV505338
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|4609695|gb|AI600534.1|AI600534
EST:     GAGACTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCTTATGCAGAGC
genomic: GAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|211161741|gb|FL193319.1|FL193319
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCACAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
EST: gi|50331233|gb|CO526359.1|CO526359
EST:     TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATG                         GCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 84

TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC


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

TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcg ... gtgttgccagGCGCAGGAGGCCACCACGCTGGGTGGTGTGAGATGGCTGCAGATGCAGAGCGCGTCCGACCTC