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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatgataaaaaaaactccacacttcttttctttcctggctgatcgatacccctggttagcactataaaacaaaatggtactacttgagtttgggtatcacgttttgtgcgtgcttcgttcttttcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA

Basic information

species Zea mays
transcript GRMZM2G322953_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 6
gttaatgataaaaaaaactccacacttcttttctttcctggctgatcgatacccctggttagcactataaaacaaaatggtactacttgagtttgggtatcacgttttgtgcgtgcttcgttcttttcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA
||   ||||  || ||      || ||||| |  ||  | |  ||| | |   | ||| |        ||||||||||||   |       ||| || | |  ||  ||| |        |  | || ||||| |||||||||  | ||| |||||||||||||| ||||||||||| || ||||| |||||||  |||||||| ||
gtctgtgattcaacaa----tgcaattcttgttcttaattg--gattggt---catggat-------caaaacaaaatggccat-------ttttggcacc-tgtactgtac--------tcttctttttgtgtagATACCAAATAGAGGAAAGATCTATTCAGTGAACGAAGGGAATGCGAAAAATTGGGATGCTCCTACAGCGAA

upper sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
gttaatgataaaaaaaactccacacttcttttctttcctggctgatcgatacccctg-gttagcactataaaacaaaatggtactacttgagtttgggtatcacgttttgtgcgtgcttcgttcttttcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA
                       | ||| | |      | |   ||  | || | |   |   | | ||    ||    | ||||    |  | |||  ||||  |||  ||  || |||          ||||||||| |||| |||||| || || |||||||| || ||||| || ||||||||||||||| | ||||| || | 
-----------------------aattcatatagactatagagtataaacacacgtatatccacgccat----cagtgggttacttgaggtatatggtaatca--tttgatgtatgattc--------tctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC
















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|32861683|gb|CF001365.1|CF001365
EST:     CTCTGGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAG                         ATACCAAAGAAAGGGAAGATCTATTCAGTGAACGAAGGGAACGCAAAAAAC
genomic: CTCTCGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAGgttaatgata ... tcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAAC
EST: gi|74034973|gb|DT535463.1|DT535463
EST:     TGACTCATCCAAATATCAAG                         ATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCTAAAAAC
genomic: TGACTCATCCAAATATCAAGgttaatgata ... tcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAAC

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: 47 (upstream exon), 46 (downstream exon)
Score: 15

CTTGTGCTGAGCACTGGGAACGGAGTCAATGGCTTCACTCTCGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAGgttaatgata ... tcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

CTTGTGCTGAGCACTGGGAACGGAGTCAATGGCTTCACTCTCGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAGgttaatgata ... tcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 184

CTTGTGCTGAGCACTGGGAACGGAGTCAATGGCTTCACTCTCGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAGgttaatgata ... tcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

CTTGTGCTGAGCACTGGGAACGGAGTCAATGGCTTCACTCTCGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAGgttaatgata ... tcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacttgagtttgggtatcacgttttgtgcgtgcttcgttcttttcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA
                                tgcttcgttcttttct  CT-rich tract
                                       ttctttt  TA-rich tract