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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactatccatttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10070.2 (Oryza sativa), 3'ss of exon 1
gtaactatccatttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
            | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
-------cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagcagCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 1
gtaactatccatttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
            | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
----gcgcgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagCAGCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
gtaactatccatttg--cttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
|| |     |  | |  ||  || ||   |  |||   |   ||   |  ||  ||      ||    |  | |   |||    |   || |  |  ||| |  | ||   || | ||  ||    |    ||        |||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||
gtgagcgcgccctcgaactcgccttaaccttgtctt--atcctccactcgatctgg----aatggaagctaggttcaatc--tggggagtataatatctgggggt-tggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG

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|76284365|gb|DV023933.1|DV023933
EST:     TGTCGGACTGTCTCGGATTCGTTCGCTGCGTGGCGGGGCGGAGCCGATTA                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: TGTCGGACTGTCTCGGATTCGTTCGCTGCGTGGCGGGGCGGAGCCGATTAgtaactatcc ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|67033527|gb|CO462276.1|CO462276
EST:     TGTCGGACTGTCTCGGATTCGTTCGCTGCGTGGCGGGGCGGAGCCGATTA                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: TGTCGGACTGTCTCGGATTCGTTCGCTGCGTGGCGGGGCGGAGCCGATTAgtaactatcc ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG

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: 18 (upstream exon), 38 (downstream exon)
Score: 5

ATTCGTCTCTAATCTGCCCTCCCCGCTCTGTCGGACTGTCTCGGATTCGTTCGCTGCGTGGCGGGGCGGAGCCGATTAgtaactatcc ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


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

ATTCGTCTCTAATCTGCCCTCCCCGCTCTGTCGGACTGTCTCGGATTCGTTCGCTGCGTGGCGGGGCGGAGCCGATTAgtaactatcc ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 9

ATTCGTCTCTAATCTGCCCTCCCCGCTCTGTCGGACTGTCTCGGATTCGTTCGCTGCGTGGCGGGGCGGAGCCGATTAgtaactatcc ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
                             tttgttt  TA-rich tract