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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG

Basic information

species Zea mays
transcript GRMZM2G003076_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 1
---gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgc--ggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG
       ||| |   | ||   |  ||  |||    |||||    || |     | |    ||   |||| ||| ||||     || | || |||||| ||| |||||||||| ||||||||||| ||||||||||| || || || |||||||| || |||||||||||||| || |||||||| ||||||||||
taaactttgggtgtttctgaatttctgatggatatcttgag----gctgggtcatgagcgttgt-aagaaatctaaatttttttggggcttgatttctcttgtagGTCCAATTGATCAGAATCGAATGTAGGGTGCCCGAATACGGGTGGACAACACAAAAGGTGTTCCATTTCCTCAACTTCCTCGTGAACGGCG

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatt--tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG
 |     | ||| |  |  | |      |||||   |||| |       |||    | |      ||||   |||  |   |  ||  ||  | | ||  |||| ||| |  |  | ||  | |  || || ||||||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||| || |
-tttctttatgaatcttcttttccataaacgaaac-agagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
lower sequence: EDP05347 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG----------
                                   | |||     |    ||    || |||   || || |||  | |    |   | |  |   |||||| ||| |  |  |  |  ||    | |||||||||||||| ||||| || ||||||||||||||  ||||||||| | | |||  | | |          
-----------------------------------gtgagtacacgagtcgtcggttccgcc---aactcggaaggctcacactgagaataattgcgcagGTACAACTGCTGCGGCTGCAGCTGCGCGTGCCAGAGTATGGCTGGACCACCCAGAAGGTGTTCCACCTTCTAAACTGCTTGGTGT-CTGTGCTGCGCTGCT

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15891 (Selaginella moellendorffii), 3'ss of exon 1
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctg--aattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG
                                  | ||  ||  |   ||   | ||  || | |  | ||    |||  |  |  ||  ||||| ||  || ||||| |  | |||||  |     ||||||| |||||||| |||||||||||||| ||||||||| | || || ||| |||| || || |
---------------------------------gtaagttagttgattcttgtaagttagctgtgtttcctatcgattttct-tcctttgtttctttt--agATCCAACTCGTTAGAATACAAATCCGGGTGCCGGAGTATGGCTGGACAACGCAGAAAGTGTTCCATCTCCTCAATTTCTTTGTAAATGGAG

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ33253 (Selaginella moellendorffii), 3'ss of exon 1
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG
                                  | ||  ||  |   ||   | ||  || | |  | ||    |||     |||  || || |   || ||||| |  | |||||  |     ||||||| |||||||| |||||||||||||| ||||||||| | || || ||| |||| || || |
---------------------------------gtaagttagttgattcttgtaagttagctgtgtttccta---tcg----attttcttcctttgttagATCCAACTCGTTAGAATACAAATCCGGGTGCCGGAGTATGGCTGGACAACGCAGAAAGTGTTCCATCTCCTCAATTTCTTTGTAAATGGAG

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23006 (Selaginella moellendorffii), 3'ss of exon 1
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG
                          | | | | |  ||   |       ||    |||   ||   ||  | | ||| || |    |||||| | |||| | ||| | ||| | ||||||  | | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| || || |
--------------------------gtatggaatccgactagttttctggtcttttctattgattcttggggaatcgtggcg----atttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

upper sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG
                         |    ||||   |  ||   |    ||    |||   ||   |   | | ||| || |    |||||| | |||| | ||| | ||| | ||||||  | | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| || || |
-------------------------gtatggaatccggctagtttgt-tggtcttttctattgattctcggggaatcgtggcg----atttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

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|149109085|gb|EE189999.2|EE189999
EST:     TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTG                         GTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG
genomic: TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG
EST: gi|211382284|gb|FL169263.1|FL169263
EST:     TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTG                         GTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG
genomic: TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG
EST: gi|148948893|gb|EC894307.2|EC894307
EST:     TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTG                         GTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG
genomic: TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG
EST: gi|149081139|gb|EE170248.2|EE170248
EST:     TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTG                         GTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG
genomic: TATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACG

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: 46 (upstream exon), 48 (downstream exon)
Score: 35

CGTGGACTGGTGGCGCGACGTCAACGAGTCGCCGCTGTGGCAGGACCGCATATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 63

CGTGGACTGGTGGCGCGACGTCAACGAGTCGCCGCTGTGGCAGGACCGCATATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 57

CGTGGACTGGTGGCGCGACGTCAACGAGTCGCCGCTGTGGCAGGACCGCATATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 107

CGTGGACTGGTGGCGCGACGTCAACGAGTCGCCGCTGTGGCAGGACCGCATATTTCACGCGCTCGCCGTGCTCTACGGCATCGTCTCGGCCGTCGCGCTGgtaagcaccc ... tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG
                                           tttctatt  CT-rich tract
                                    tgtttaatttctatt  TA-rich tract